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From: <no...@us...> - 2010-10-12 21:00:28
|
Revision: 23953
http://gmod.svn.sourceforge.net/gmod/?rev=23953&view=rev
Author: nomi
Date: 2010-10-12 21:00:13 +0000 (Tue, 12 Oct 2010)
Log Message:
-----------
Most of the changes in this doc were made in place on the Apollo web server but were never committed.
95% of these are simply conversions to strictly correct HTML (e.g., <br> rather than <BR>).
I have also updated the Apollo mailing list URL and a few other hardcoded URLs.
Modified Paths:
--------------
apollo/trunk/doc/html/userguide.html
Modified: apollo/trunk/doc/html/userguide.html
===================================================================
--- apollo/trunk/doc/html/userguide.html 2010-10-12 17:32:38 UTC (rev 23952)
+++ apollo/trunk/doc/html/userguide.html 2010-10-12 21:00:13 UTC (rev 23953)
@@ -1,175 +1,176 @@
-<html>
+<html><head>
+<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
-<head>
+
<title>Apollo User Guide</title>
-</head>
+</head><body bgcolor="#ffffff">
-<body bgcolor="#FFFFFF">
+<h1 align="center">Apollo User Guide </h1>
-<H1 align=center>Apollo User Guide </H1>
+<center><img src="images/apollosplash.jpg" height="240" width="529">
+<h2>Version 1.11.x<br>October 2009</h2>
+</center>
-<CENTER><img SRC="images/apollosplash.gerry.jpg" width=529 height=240>
-<h2>Version 1.10.x<br>February 2009</h2>
-</CENTER>
-
<h1>Table of Contents</h1>
-<a href="#Introduction">Introduction</a><BR>
-<UL>
-<LI><a href="#Community">The Apollo community</a><BR>
-<LI><a href="#Bugs">Reporting bugs</a><BR>
-<LI><a href="#mailing">Apollo mailing list</a><BR>
-</UL>
-<a href="#Download">Installing Apollo</a><BR>
+<a href="#Introduction">Introduction</a><br>
+<ul>
+<li><a href="#Community">The Apollo community</a><br>
+</li><li><a href="#Bugs">Reporting bugs</a><br>
+</li><li><a href="#mailing">Apollo mailing list</a><br>
+</li></ul>
+<a href="#Download">Installing Apollo</a><br>
<a href="#StartingUp">Starting up</a>
-<UL>
-<LI><a href="#StartingUnix">Unix</a><BR>
-<LI><a href="#StartingWindows">Windows or Mac</a><BR>
-<LI><a href="#FirstView">The first view of Apollo</a>
-<LI><a href="#stdout">Text output from Apollo</a>
-</UL>
+<ul>
+<li><a href="#StartingUnix">Unix</a><br>
+</li><li><a href="#StartingWindows">Windows or Mac</a><br>
+</li><li><a href="#FirstView">The first view of Apollo</a>
+</li><li><a href="#stdout">Text output from Apollo</a>
+</li></ul>
<a href="#Loading">Loading Data</a>
-<UL>
-<LI><a href="#ReadingXML">Reading Drosophila annotations</a><BR>
-<LI><a href="#ChadoXMLAdapter">Reading Chado XML files</a><BR>
-<LI><a href="#ChadoAdapter">Reading data directly from a Chado database</a><BR>
-<LI><a href="#ReadingGFF">Reading Ensembl GFF files</a><BR>
-<LI><a href="#ReadingGFF3">Reading GFF3 files</a><BR>
-<LI><a href="#Reading_Ensembl_via_ensj">Reading Ensembl schema databases</a><BR>
-<LI><a href="game-synteny.html">Reading cross-species comparative data in
+<ul>
+<li><a href="#ReadingXML">Reading Drosophila annotations</a><br>
+</li><li><a href="#ChadoXMLAdapter">Reading Chado XML files</a><br>
+</li><li><a href="#ChadoAdapter">Reading data directly from a Chado database</a><br>
+</li><li><a href="#ReadingGFF">Reading Ensembl GFF files</a><br>
+</li><li><a href="#ReadingGFF3">Reading GFF3 files</a><br>
+</li><li><a href="#Reading_Ensembl_via_ensj">Reading Ensembl schema databases</a><br>
+</li><li><a href="http://apollo.berkeleybop.org/current/game-synteny.html">Reading cross-species comparative data in
GAME XML format and from chado JDBC
- (synteny viewer)</a><BR>
-<LI><a href="#ReadingGenbank">Reading GenBank or EMBL data</a><BR>
-<LI><a href="#AnalysisAdapter">Reading raw analysis results</a><BR>
-<LI><a href="#Layering">Layering data</a><BR>
-<LI><a href="#CommandLine">Command-line arguments</a><BR>
-<LI><a href="#Styles">Styles</a><BR>
-</UL>
+ (synteny viewer)</a><br>
+</li><li><a href="#ReadingGenbank">Reading GenBank or EMBL data</a><br>
+</li><li><a href="#AnalysisAdapter">Reading raw analysis results</a><br>
+</li><li><a href="#Layering">Layering data</a><br>
+</li><li><a href="#CommandLine">Command-line arguments</a><br>
+</li><li><a href="#Styles">Styles</a><br>
+</li></ul>
<a href="#DisplayPanels">The display panels</a>
-<UL>
-<LI><a href="#MainWindow">The main window</a>
-<UL>
-<LI><a href="#AnnotationsVsResults">Annotations vs. results</a><BR>
-<LI><a href="#Splitters">Splitters</a><BR>
-<LI><a href="#Zooming">Zooming and scrolling</a><BR>
-<LI><a href="#MovingMouse">Moving using the mouse--centering the display</a><BR>
-<LI><a href="#ZoomToSelected">Zoom to selected</a><BR>
-<LI><a href="#GuideLine">The guide line</a><BR>
-<LI><a href="#ShowReverse">Showing reverse complement</a><BR>
-<LI><a href="#ShowStrand">Forward and reverse strands</a><BR>
-<LI><a href="#FeatureDetail">Feature detail panels</a><BR>
-</UL>
-<li><a href="#Preferences">Preferences editor</a></li>
-<LI><a href="#ApolloWindows">Apollo windows</a><BR>
-<LI><a href="#WebBrowser">Apollo and Web browsers</a><BR>
-<LI><a href="#Selection">Selection</a>
-<UL>
-<LI><a href="#SingleFeature">Selecting a single feature</a><BR>
-<LI><a href="#MultipleFeature">Selecting multiple features</a><BR>
-<LI><a href="#ShiftSelecting">Adding to a selection</a><BR>
-<LI><a href="#Deselecting">Deselecting</a><BR>
-</UL>
-<LI><a href="#Annotations">Finding out more about annotations and results</a><BR>
-<UL>
-<LI><a href="#Linkout">Get info about features via Web</a><BR>
-<LI><a href="#AnnotationInfo">Annotation info</a><BR>
-<LI><a href="#AnnotationTree">The annotation tree</a><BR>
-<LI><a href="#AnnotationMenu">Annotation menu</a><BR>
-<LI><a href="#Bookmarks">Bookmarks</a><BR>
-</UL>
-</UL>
-</UL>
+<ul>
+<li><a href="#MainWindow">The main window</a>
+<ul>
+<li><a href="#AnnotationsVsResults">Annotations vs. results</a><br>
+</li><li><a href="#Splitters">Splitters</a><br>
+</li><li><a href="#Zooming">Zooming and scrolling</a><br>
+</li><li><a href="#MovingMouse">Moving using the mouse--centering the display</a><br>
+</li><li><a href="#ZoomToSelected">Zoom to selected</a><br>
+</li><li><a href="#GuideLine">The guide line</a><br>
+</li><li><a href="#ShowReverse">Showing reverse complement</a><br>
+</li><li><a href="#ShowStrand">Forward and reverse strands</a><br>
+</li><li><a href="#FeatureDetail">Feature detail panels</a><br>
+</li></ul>
+</li><li><a href="#TypesPanel">The types panel</a><br>
+</li><li><a href="#Preferences">Preferences editor</a></li>
+<li><a href="#ApolloWindows">Apollo windows</a><br>
+</li><li><a href="#WebBrowser">Apollo and Web browsers</a><br>
+</li><li><a href="#Selection">Selection</a>
+<ul>
+<li><a href="#SingleFeature">Selecting a single feature</a><br>
+</li><li><a href="#MultipleFeature">Selecting multiple features</a><br>
+</li><li><a href="#ShiftSelecting">Adding to a selection</a><br>
+</li><li><a href="#Deselecting">Deselecting</a><br>
+</li></ul>
+</li><li><a href="#Annotations">Finding out more about annotations and results</a><br>
+<ul>
+<li><a href="#Linkout">Get info about features via Web</a><br>
+</li><li><a href="#AnnotationInfo">Annotation info</a><br>
+</li><li><a href="#AnnotationTree">The annotation tree</a><br>
+</li><li><a href="#AnnotationMenu">Annotation menu</a><br>
+</li><li><a href="#Bookmarks">Bookmarks</a><br>
+</li></ul>
+</li></ul>
+
<a href="#SearchFunctions">Search functions</a>
-<UL>
-<LI><a href="#FindingBase">Finding a specific base</a><BR>
-<LI><a href="#FindingFeature">Finding a feature</a><BR>
-<LI><a href="#FindingSequence">Finding a subsequence</a><BR>
-<LI><a href="#RegExp">Using regular expressions</a><BR>
-</UL>
+<ul>
+<li><a href="#FindingBase">Finding a specific base</a><br>
+</li><li><a href="#FindingFeature">Finding a feature</a><br>
+</li><li><a href="#FindingSequence">Finding a subsequence</a><br>
+</li><li><a href="#RegExp">Using regular expressions</a><br>
+</li></ul>
<a href="#FeatureDisplay">Specifying which features to display</a>
-<UL>
-<LI><a href="#CollapsedView">Collapsed view</a><BR>
-<LI><a href="#ExpandedView">Expanded view</a><BR>
-<LI><a href="#HidingFeature">Hiding features</a><BR>
-<LI><a href="#ShowingFeature">Showing features</a><BR>
-<LI><a href="#ResizeFeature">Resizing features</a><BR>
-<LI><a href="#DashSets">Showing sequencing gaps in ESTs<BR>
-<LI><a href="#NewSeqs">Hits to new sequences<BR>
-<LI><a href="#FeatureLabels">Showing feature labels</a><BR>
-<LI><a href="#BackgroundColor">Background colors</a><BR>
-<LI><a href="#EvidencePanelOrientation">Changing orientation of evidence panel</a><BR>
-</UL>
+<ul>
+<li><a href="#CollapsedView">Collapsed view</a><br>
+</li><li><a href="#ExpandedView">Expanded view</a><br>
+</li><li><a href="#HidingFeature">Hiding features</a><br>
+</li><li><a href="#ShowingFeature">Showing features</a><br>
+</li><li><a href="#ResizeFeature">Resizing features</a><br>
+</li><li><a href="#DashSets">Showing sequencing gaps in ESTs<br>
+</a></li><li><a href="#NewSeqs">Hits to new sequences<br>
+</a></li><li><a href="#FeatureLabels">Showing feature labels</a><br>
+</li><li><a href="#TypesPanelControl">Using the Types panel to control display of features</a><br>
+</li><li><a href="#BackgroundColor">Background colors</a><br>
+</li><li><a href="#EvidencePanelOrientation">Changing orientation of evidence panel</a><br>
+</li></ul>
<a href="#SequenceLevelFeatures">Sequence level features</a>
-<UL>
-<LI><a href="#ShowSequence">Showing the genomic sequence</a><BR>
-<LI><a href="#SequenceWindow">Translating and saving sequence</a><BR>
-<UL>
-<LI><a href="#SavingSeq">Saving whole sequence</a><BR>
-</UL>
-<LI><a href="#StartStopCodons">Start and stop codons</a><BR>
-<LI><a href="#EdgeMatches">Edge matches</a><BR>
-<LI><a href="#SpliceSites">Non-consensus splice sites</a></h3>
-<LI><a href="#Analyses">Analyses: GC content and restriction sites</a><BR>
-<li><a href="#Analyses-remote">Analyses: Remote analysis services</a></li>
<ul>
+<li><a href="#ShowSequence">Showing the genomic sequence</a><br>
+</li><li><a href="#SequenceWindow">Translating and saving sequence</a><br>
+<ul>
+<li><a href="#SavingSeq">Saving whole sequence</a><br>
+</li></ul>
+</li><li><a href="#StartStopCodons">Start and stop codons</a><br>
+</li><li><a href="#EdgeMatches">Edge matches</a><br>
+</li><li><a href="#SpliceSites">Non-consensus splice sites</a>
+</li><li><a href="#Analyses">Analyses: GC content and restriction sites</a><br>
+</li><li><a href="#Analyses-remote">Analyses: Remote analysis services</a></li>
+<ul>
<li><a href="#NCBI-BLAST">NCBI BLAST</a></li>
<li><a href="#NCBI-PRIMER-BLAST">NCBI Primer BLAST</a></li>
</ul>
-<LI><a href="#Jalview">Viewing alignments</a><BR>
-<LI><a href="#Graphs">Viewing graph data</a><BR>
-</UL>
-<a href="#Printing">Printing to file - Postscript output</a><BR>
-<a href="#Links">Links to useful sequence analysis sites</a><BR>
-<a href="#Help">Apollo help</a><BR>
-<a href="#SoftwareUpdates">Checking for Apollo software updates</a><BR>
+<li><a href="#Jalview">Viewing alignments</a><br>
+</li><li><a href="#Graphs">Viewing graph data</a><br>
+</li></ul>
+<a href="#Printing">Printing to file - Postscript output</a><br>
+<a href="#Links">Links to useful sequence analysis sites</a><br>
+<a href="#Help">Apollo help</a><br>
+<a href="#SoftwareUpdates">Checking for Apollo software updates</a><br>
<a href="#MouseFunctions">Summary of mouse functions</a>
-<P>
+<p>
<a href="#Edit">Using Apollo to edit annotations</a>
-<UL>
-<LI><a href="#Saving">Saving your annotations</a><BR>
-<LI><a href="#Autosaving">Autosaving</a><BR>
-<LI><a href="#TranscriptColoring">Transcript coloring</a><BR>
-<LI><a href="#CreatingGene">Creating a new annotation</a><BR>
-<LI><a href="#ModifyingGene">Modifying gene models</a><BR>
-<LI><a href="#FlippingResult">Changing the strand of a result</a><BR>
-<LI><a href="#ResultTag">Tagging a result with a comment</a><BR>
-<LI><a href="#AnnotationText">Editing annotation text</a><BR>
-<LI><a href="#ExonDetailEditor">Exon detail editor</a><BR>
-<UL>
-<LI><a href="#EDEConfig">Configuration options for the Exon Detail Editor</a><BR>
-<LI><a href="#EDEUsing">Using the Exon Detail Editor</a><BR>
-<LI><a href="#frame_shifts">Setting translational frame shifts</a><BR>
-<LI><a href="#seq_errors">Indicating genomic sequencing errors</a><BR>
-</UL>
-<LI><a href="#SequenceAligner">Sequence Aligner</a><BR>
-<UL>
-<LI><a href="#SEQDNAView">The DNA view for the Sequence Aligner</a><BR>
-<LI><a href="#SEQAAView">The AA view for the Sequence Aligner</a><BR>
-</UL>
-</UL>
-<a href="#Configuration">Configuring Apollo</a><BR>
-<UL>
-<LI><a href="#apollo.cfg">apollo.cfg</a><BR>
-<LI><a href="#StyleFiles">Style files</a><BR>
-<LI><a href="#TiersFiles">Tiers files</a><BR>
-</UL>
-<a href="#source">Getting the source code</a><BR>
-<a href="#Adapting">Adapting Apollo</a><BR>
-<a href="#Contributed">Contributed Apollo Documentation</a><BR>
-<a href="#acknowledgements">Acknowledgements</a><BR>
+</p><ul>
+<li><a href="#Saving">Saving your annotations</a><br>
+</li><li><a href="#Autosaving">Autosaving</a><br>
+</li><li><a href="#TranscriptColoring">Transcript coloring</a><br>
+</li><li><a href="#CreatingGene">Creating a new annotation</a><br>
+</li><li><a href="#ModifyingGene">Modifying gene models</a><br>
+</li><li><a href="#FlippingResult">Changing the strand of a result</a><br>
+</li><li><a href="#ResultTag">Tagging a result with a comment</a><br>
+</li><li><a href="#AnnotationText">Editing annotation text</a><br>
+</li><li><a href="#ExonDetailEditor">Exon detail editor</a><br>
+<ul>
+<li><a href="#EDEConfig">Configuration options for the Exon Detail Editor</a><br>
+</li><li><a href="#EDEUsing">Using the Exon Detail Editor</a><br>
+</li><li><a href="#frame_shifts">Setting translational frame shifts</a><br>
+</li><li><a href="#seq_errors">Indicating genomic sequencing errors</a><br>
+</li></ul>
+</li><li><a href="#SequenceAligner">Sequence Aligner</a><br>
+<ul>
+<li><a href="#SEQDNAView">The DNA view for the Sequence Aligner</a><br>
+</li><li><a href="#SEQAAView">The AA view for the Sequence Aligner</a><br>
+</li></ul>
+</li></ul>
+<a href="#Configuration">Configuring Apollo</a><br>
+<ul>
+<li><a href="#apollo.cfg">apollo.cfg</a><br>
+</li><li><a href="#StyleFiles">Style files</a><br>
+</li><li><a href="#TiersFiles">Tiers files</a><br>
+</li></ul>
+<a href="#source">Getting the source code</a><br>
+<a href="#Adapting">Adapting Apollo</a><br>
+<a href="#Contributed">Contributed Apollo Documentation</a><br>
+<a href="#acknowledgements">Acknowledgements</a><br>
-<hr size=0>
+<hr size="0">
<h1>
-<a NAME="Introduction"></a>Introduction</h1>
-<P>
+<a name="Introduction"></a>Introduction</h1>
+<p>
Apollo is a genomic annotation viewer and editor. It was originally
developed as a collaboration between the Berkeley Drosophila Genome Project
(part of the FlyBase consortium)
and The Sanger Institute in Cambridge, UK.
It was used by the
-FlyBase biologists to construct the <a href=http://www.fruitfly.org/annot/release3.html>Release 3</a> and 4 annotations</a> on the finished
+FlyBase biologists to construct the <a href="http://www.fruitfly.org/annot/release3.html">Release 3</a> and 4 annotations on the finished
<i>Drosophila melanogaster</i> genome, and has also been a primary vehicle
for sharing these annotations with the community.
-<P>
+</p><p>
Apollo allows researchers to explore genomic
annotations at many levels of detail, and to perform expert annotation
curation, all in a graphical environment.
@@ -177,38 +178,38 @@
application that is easy to install and run on Windows, Mac OS X, or any Unix-type system
(including Linux).
Apollo is currently supported by NIH grant 1R01GM080203-01 from the National Institute of General Medical Sciences (NIGMS).
-<P>
+</p><p>
The current Apollo team is:
-<UL>
+</p><ul>
<li>Ed Lee (leader and chief developer)</li>
<li>Nomi Harris</li>
-<li>Mark Gibson</li>
<li>Suzanna Lewis</li>
-</UL>
-<P>The original Apollo developers were:
-<P>
-<UL>
+</ul>
+<p>Previous Apollo developers were:
+</p><p>
+</p><ul>
<li>Steve Searle</li>
<li>Michele Clamp</li>
<li>Suzanna Lewis</li>
<li>John Richter</li>
-</UL>
-<P>
+<li>Mark Gibson</li>
+</ul>
+<p>
Other contributors have included:
-<UL>
-<LI>Sima Misra</LI>
+</p><ul>
+<li>Sima Misra</li>
<li>Guanming Wu</li>
<li>Jonathan Crabtree (Chado JDBC adapter)</li>
<li>Vivek Iyer</li>
<li>Craig Melsopp</li>
-<LI>Chris Mungall</LI>
+<li>Chris Mungall</li>
<li>Colin Wiel</li>
<li>Chris Wilks</li>
<li>Olivier Arnaiz</li>
-<LI>and all the FlyBase curators</LI>
-</UL>
+<li>and all the FlyBase curators</li>
+</ul>
-<a NAME="Community"></a><h3>The Apollo community</h3>
+<a name="Community"></a><h3>The Apollo community</h3>
An increasing number of research groups are using Apollo as a starting
point for customizing their own annotation visualization tool. Because
@@ -216,68 +217,66 @@
groups working on different organisms (fruitfly and human) with different
types of data, it was specifically designed to be flexible and
extensible.
-The <a href=http://www.gmod.org>Generic Model Organism Database (GMOD) project</a>, which
+The <a href="http://www.gmod.org/">Generic Model Organism Database (GMOD) project</a>, which
aims to provide a complete ready-to-use toolkit for analyzing whole
genomes, has adopted Apollo as its annotation workbench.
Apollo is Open Source; the Apollo source code is all available at
-<a href=http://sourceforge.net/project/showfiles.php?group_id=27707>
-SourceForge</a> as part of the <a href=http://sourceforge.net/projects/gmod/>GMOD project</a>.
+<a href="http://sourceforge.net/project/showfiles.php?group_id=27707">
+SourceForge</a> as part of the <a href="http://sourceforge.net/projects/gmod/">GMOD project</a>.
-<a NAME="Bugs"></a><h3>Reporting bugs</h3>
+<a name="Bugs"></a><h3>Reporting bugs</h3>
Apollo is still under active development, and there are still many
bugs--some we know about, and some we don't.
-The bugs we know about are listed in the <a href="http://sourceforge.net/tracker/?func=browse&group_id=27707&atid=462763">SourceForge Apollo bug tracker</a>.
+The bugs we know about are listed in the <a href="http://sourceforge.net/tracker/?func=browse&group_id=27707&atid=462763">SourceForge Apollo bug tracker</a>.
If you encounter a problem that is not in the list of reported bugs, please
-<a href=http://sourceforge.net/tracker/?func=add&group_id=27707&atid=462763>
-submit a new bug report</a> or ask on the <a href=#mailing>Apollo mailing list</a>.
+<a href="http://sourceforge.net/tracker/?func=add&group_id=27707&atid=462763">
+submit a new bug report</a> or ask on the <a href="#mailing">Apollo mailing list</a>.
Please be as specific as possible when you
report bugs--tell us which version of Apollo you're running, what dataset you were looking at, what operating system
you're on (including the version number), and what you did that caused the bug. Also send us the
-output from the Java console (see the section on <a href=#stdout>Text output
+output from the Java console (see the section on <a href="#stdout">Text output
from Apollo</a>).
-<P>
+<p>
When you report a bug, <b>be sure to include your email address</b>. We may
need to ask you questions in order to track down the bug, and you'll probably want
to know when we've fixed it. You will not be added to any mailing lists or sent
any other correspondence.
-<P>
+</p><p>
Mac users, please note: the top-level menu item that says "About Apollo" purports
to tell you the Apollo version number, but in fact it's telling you the version number
of the installer. To get the correct Apollo version number, use the "About" item from Apollo's
Help menu.
-<a NAME="mailing"></a><h3>Apollo mailing list</h3>
+<a name="mailing"></a></p><h3>Apollo mailing list</h3>
-If you are interested in discussing Apollo with other users, you can join the <a
-href=http://mail.fruitfly.org/mailman/listinfo/apollo>Apollo mailing list</a>. Traffic is low,
+If you are interested in discussing Apollo with other users, you can join the <a href="https://lists.lbl.gov/sympa/info/apollo">Apollo mailing list</a>. Traffic is low,
and your email address will not be made publicly visible or used for any other purpose. In order to reduce spam on the
list, you must join in order to send messages to the list.
-To unsubscribe from the mailing list, use <a href=http://mail.fruitfly.org/mailman/listinfo/apollo>the same Web form</a>.
+To unsubscribe from the mailing list, use <a href="https://lists.lbl.gov/sympa/info/apollo">the same Web form</a>.
-<P>
-<h1>
-<a NAME="Download"></a>Installing Apollo</h1>
-<P>
+<p>
+</p><h1>
+<a name="Download"></a>Installing Apollo</h1>
+<p>
Apollo is a Java application that you can download and run on your
computer (Windows, Linux, or Mac OS X--earlier Mac versions are not
-supported). You can get Apollo <a href=http://www.fruitfly.org/annot/apollo/>here</a>.
+supported). You can get Apollo <a href="/">here</a>.
When you
install Apollo, a JVM is bundled with it, unless you are on Mac OS X.
-<h3>Getting the appropriate Java on a Mac</h3>
+</p><h3>Getting the appropriate Java on a Mac</h3>
Apollo is now set up to run with JDK1.5 or 1.6, so make sure you have one of these versions of Java installed.
-You will need Mac OS X 10.4+ to install JDK1.5. Please see <a href=http://www.apple.com/softwareupdate>Apple's instructions on how to do this</a>, using Software Updates.
+You will need Mac OS X 10.4+ to install JDK1.5. Please see <a href="http://www.apple.com/softwareupdate">Apple's instructions on how to do this</a>, using Software Updates.
(Apollo cannot run on older versions of Mac OS X.)
-<P>
+<p>
Some versions of Mac OS X have Java issues--standalone
Java applications (such as Apollo) may unexpectedly quit or not
launch. You can perform a simple test to verify whether your computer is
experiencing this issue. If it is, you will need to reinstall one or two
-Java software updates to resolve the issue. Please <a target=_new
-href=http://docs.info.apple.com/article.html?artnum=301380>look here</a>
+Java software updates to resolve the issue. Please <a target="_new" href="http://docs.info.apple.com/article.html?artnum=301380">look here</a>
for help.
-<p>
+</p><p>
-<h3>Memory use</h3>
+</p><h3>Memory use</h3>
Apollo uses a lot of memory, largely due to the sheer size of the
annotation data. In order to use Apollo, your computer will need to have
@@ -285,17 +284,19 @@
will probably find that if you try to run more than one instance of
Apollo at the same time, performance will suffer. Also note that if you
load a very large region, Apollo will use up more memory.
-<P>
+<p>
Keep in mind that other applications running on your
-computer also use memory, so you will get better performance if you shut down other applications (Photoshop, Word, etc.) before you launch Apollo.
+computer also use memory, so you will get better performance if you shut
+ down other applications (Photoshop, Word, etc.) before you launch
+Apollo.
-<P>
+</p><p>
Apollo checks twice a minute to make sure you still have enough free memory.
If the free memory is getting very low (less than 5% of the the value
defined as "Memory" in apollo.cfg), you will get a warning. If you have
done or are planning to do any editing, you should save your work and
then quit and restart Apollo.
-<P>
+</p><p>
If you load many large regions into Apollo (such as cytological bands),
it is possible that it will run out of memory despite the memory checks. Usually the behavior
you'll see if this happens is that it will freeze up during loading, but
@@ -303,51 +304,54 @@
Java console, you may see "java.lang.OutOfMemoryError". If this happens,
you should exit Apollo and restart.
-<h1>
-<a NAME="StartingUp"></a>Starting up</h1>
-<P>
-<h2>
-<a NAME="StartingUnix"></a>Unix</h2>
+</p><h1>
+<a name="StartingUp"></a>Starting up</h1>
+<p>
+</p><h2>
+<a name="StartingUnix"></a>Unix</h2>
From the directory where Apollo is installed, type
-<UL>
+<ul>
<pre>./Apollo</pre>
-</UL>
+</ul>
You should also be able to run Apollo from other directories by specifying the full path.
-<P>
-<h2>
-<a NAME="StartingWindows"></a>Windows or Mac</h2>
+<p>
+</p><h2>
+<a name="StartingWindows"></a>Windows or Mac</h2>
Select the Apollo icon from your desktop or dock.
-<P>
-<B>Note for Mac users running Panther (10.3)</b>:
+<p>
+<b>Note for Mac users running Panther (10.3)</b>:
Some security-related software updates on Panther interfere
with Java and prevent Apollo from launching from the shortcut (you will see
the icon bounce a few times and then stop, and no Apollo window comes up). We are looking into
how to address that, but there are two workarounds. Either:
-<LI> Upgrade your Mac to Tiger or Leopard; or<BR>
-<LI> Launch Apollo from the command line. First, start a Terminal window (Applications -> Utilities -> Terminal). In the Terminal window, cd to the directory where you installed Apollo, usually /Applications/Apollo, and type ./bin/apollo (note the lowercase a):<BR>
+</p><li> Upgrade your Mac to Leopard or Snow Leopard; or<br>
+</li><li> Launch Apollo from the command line. First, start a Terminal
+window (Applications -> Utilities -> Terminal). In the Terminal
+window, cd to the directory where you installed Apollo, usually
+/Applications/Apollo, and type ./bin/apollo (note the lowercase a):<br>
<pre><dd>cd /Applications/Apollo
-<dd>./bin/apollo</pre>
+</dd><dd>./bin/apollo</dd></pre>
You will see the text output from Apollo in the Terminal window, and an Apollo
window should come up.
-<P>Note: if you want to run Apollo from the command line, it will not be able
+<p>Note: if you want to run Apollo from the command line, it will not be able
to control which version of the Java virtual machine your Mac defaults
to using (as it does if you run the installed Apollo). Please make sure that you are set up to use JDK version 1.5 or 1.6,
rather than 1.3, which is the default on some older Macs.
<br>
-<h2>
-<a NAME="FirstView"></a>The first view of Apollo</h2>
-<P>
+</p><h2>
+<a name="FirstView"></a>The first view of Apollo</h2>
+<p>
When Apollo starts up you should see the Apollo splashscreen, which will stay up
for a few seconds while the Apollo software loads.
-<P>
-<center><img SRC="images/apollosplash.gerry.jpg" alt="Apollo splash screen" width=529 height=240></center>
-<P>
+</p><p>
+</p><center><img src="images/apollosplash.jpg" alt="Apollo splash screen" height="240" width="529"></center>
+<p>
You should then see a window offering various ways to find the region you
are interested in. These will be discussed shortly.
-<P>
-<center><img SRC="images/loadgamefile.gif" width=601 height=186></center>
-<P>
-<h2><a NAME="stdout"></a>Text output from Apollo</h2>
+</p><p>
+</p><center><img src="images/loadgamefile.gif" height="186" width="601"></center>
+<p>
+</p><h2><a name="stdout"></a>Text output from Apollo</h2>
Sometimes it's important to see the text output from Apollo--the messages
it prints to inform the user about what it's doing.
This is particularly
@@ -357,11 +361,15 @@
$APOLLO_ROOT/logs/stdout.log<br>
$APOLLO_ROOT/logs/stderr.log<br>
<br>
-where $APOLLO_ROOT is the location where Apollo was installed. Note that stdout/stderr are only captured into log files if you installed Apollo with the installer program. If you are running Apollo directly from the source code, stdout/stderr won't be redirected and will display on the terminal where you're invoking Apollo from.<br>
+where $APOLLO_ROOT is the location where Apollo was installed. Note
+that stdout/stderr are only captured into log files if you installed
+Apollo with the installer program. If you are running Apollo directly
+from the source code, stdout/stderr won't be redirected and will display
+ on the terminal where you're invoking Apollo from.<br>
<h1>
-<a NAME="Loading"></a>Loading Data</h1>
-<P>
-<h3><a NAME="ReadingXML"></a>Reading data from a file</h3>
+<a name="Loading"></a>Loading Data</h1>
+<p>
+</p><h3><a name="ReadingXML"></a>Reading data from a file</h3>
The oldest and, in many ways, most fully-functional data adapter in
Apollo is the GAME XML adapter. The simplest
way to try out Apollo is to choose the GAME XML adapter from the "Choose
@@ -369,36 +377,36 @@
contains computational results and curated annotations for a region of the
D. melanogaster genome), which is included with the Apollo distribution.
-<h3><a NAME="ReadingXML"></a>Reading Drosophila annotation data</h3>
+<h3><a name="ReadingXML"></a>Reading Drosophila annotation data</h3>
The annotations on the <i>Drosophila melanogaster</i> genome are now stored in a version of
the Chado XML format. Drosophila annotation data in Chado XML format can
be read from a file or pulled transparently across the network from the
FlyBase annotation database.
-<P>
+<p>
Apollo provides several ways to search for the Drosophila region you are interested in:
-<UL>
-<LI>Filename (e.g., <i>data/CG16983.chado.xml</i>)--filenames can use absolute or relative
+</p><ul>
+<li>Filename (e.g., <i>data/CG16983.chado.xml</i>)--filenames can use absolute or relative
paths (relative paths are taken to refer to files inside the Apollo directory). Please
note that if you use the Browse button to select a file, you still need to hit the "Ok"
button to begin loading the file. (You can also enter an URL as a
filename.)
-<P> A quick tip about the file chooser that is invoked by the Browse button: by default, it comes up in a mode where
+<p> A quick tip about the file chooser that is invoked by the Browse button: by default, it comes up in a mode where
you scroll horizontally to see all the available directories and files. If you
prefer vertical scrolling, click on the icon at the top right of the chooser window,
which looks like two little squares, each followed by a line.
-<LI>Gene name (e.g., <i>cact</i>)--finds the region surrounding the gene
-<LI>Cytological band (e.g., <i>40B</i>). Warning: these are big and use
+</p></li><li>Gene name (e.g., <i>cact</i>)--finds the region surrounding the gene
+</li><li>Cytological band (e.g., <i>40B</i>). Warning: these are big and use
up a lot of memory.
-<LI>Location: chromosome arm, start and end position (e.g., <i>3R 100000 300000</i>)
-</UL>
-<P>
+</li><li>Location: chromosome arm, start and end position (e.g., <i>3R 100000 300000</i>)
+</li></ul>
+<p>
By clicking on the tabs labeled "Gene", "Cytology", etc., you can decide how you
want to look for the region of interest. Note that the FlyBase server will return
the scaffold (~350Kb region) that is closest to your query, not the precise region
you requested.
-<P>
-<center><img SRC="images/load-chado-xml.gif" width=710 height=248></center>
-<P>
+</p><p>
+</p><center><img src="images/load-chado-xml.gif" height="248" width="710"></center>
+<p>
Note that except for the "File" search, all the searches go over the network to
get the Drosophila annotations from the FlyBase server, so you must be connected to
the internet to use them. Sometimes it takes a while to fetch the data across the
@@ -407,40 +415,40 @@
message is that you might have a firewall that prevents the data from getting to
your computer. If you use a proxy, be sure to set the proxy by clicking the "Proxy settings"
button before trying to load data.
-<P>
+</p><p>
If you'd like to download all the FlyBase Drosophila
annotation data to your computer so you can then access it locally via the File tab,
-please visit <a target=_new href=http://flybase.bio.indiana.edu/annot/>http://flybase.bio.indiana.edu/annot/</a>.
+please visit <a target="_new" href="http://flybase.bio.indiana.edu/annot/">http://flybase.bio.indiana.edu/annot/</a>.
-<h3> <a NAME="ChadoXMLAdapter"></a>Reading Chado XML or GAME XML files</a></h3>
+</p><h3> <a name="ChadoXMLAdapter"></a>Reading Chado XML or GAME XML files</h3>
The Chado XML adapter lets you read and write FlyBase-style
Chado XML files with no macros. A sample Chado XML file containing some Drosophila
annotations, data/CG16893.chado.xml, is included with the Apollo distribution.
-<P>
+<p>
The Chado XML adapter has not yet been generalized for use with
non-FlyBase data. Also, it cannot yet handle macros, and it doesn't yet deal with
some types of "non-Apollo" data such as feature_cvterms.
Theoretically, you can use Apollo as a converter between Chado XML and GAME, but we are still
-debugging that conversion. Please see <a target=todo href=../todo>doc/todo</a>
+debugging that conversion. Please see <a target="todo" href="http://apollo.berkeleybop.org/todo">doc/todo</a>
for a list of known issues with the Chado XML adapter.
-<P>
-The <a href=http://www.fruitfly.org/annot/apollo/game.rng.txt>GAME XML</a> adapter
+</p><p>
+The <a href="/game.rng.txt">GAME XML</a> adapter
was written to handle Drosophila data in the older GAME XML format. You should be
able to use it to read other types of annotation data in GAME XML format, but you
will need to change the tiers file.
-<p>
+</p><p>
You can also write out two different GAME XML versions (1.0 and
1.1). This is
configurable in style--set DO_ONE_LEVEL_ANNOTS "false" makes it save
1.0, otherwise it saves 1.1.
-<p>
+</p><p>
-<h3> <a NAME="ChadoAdapter"></a>Reading data directly from a Chado database</h3>
+</p><h3> <a name="ChadoAdapter"></a>Reading data directly from a Chado database</h3>
The Chado JDBC adapter allows Apollo to read annotation data directly from a Chado
database. Using this adapter to read data from your Chado database will require modification
of some configuration files.
-<P>
+<p>
If you want to try reading Drosophila annotations from the FlyBase Chado server (which might
or might not still be running), select "Chado" from the data adapter
list. There is only one database to choose: "FlyBase Chado Indiana
@@ -449,34 +457,34 @@
the Sequence Ontology term for a scaffold). In the "Region ID" box, enter the
gene name (if you selected type gene) or scaffold ID (if you selected
golden_path_region). An example of a fruitfly gene is "cact". An
-example scaffold ID is AE003603. <p>
+example scaffold ID is AE003603. </p><p>
The Chado adapter has known bugs that are described in
-<a target=todo href=../chado/chado-jdbc-todo>doc/chado/chado-jdbc-todo</a>. For example,
+<a target="todo" href="http://apollo.berkeleybop.org/chado/chado-jdbc-todo">doc/chado/chado-jdbc-todo</a>. For example,
if you request a region that doesn't exist, Apollo will
seize up. Also the dashed contig result lines that are present from
the GAME Adapter are not coming up yet. See chado-jdbc-todo for the full listing.
-<P>
+</p><p>
Also, if you ask the server for data by chromosome region (e.g.,
2L:10000-20000), you may get an entire scaffold that includes the requested
gene or region--not the actual region requested. This is a bug in the
server, not Apollo (as of v. 1.6.5).
-<P>
+</p><p>
The Chado data adapter can do direct-to-database writeback. It converts the transactions to
updates to the chado database, so only edited features are updated in the
database. Currently this is working with the Chado Rice database (at Cold
Spring Harbor). Adapting it to other Chado databases shouldn't be too
hard.
-<P>
+</p><p>
If you are a developer who wants to enable Apollo to access your own Chado database,
-please see the section about <a href=#CustomizingChadoAdapter>customizing the
+please see the section about <a href="#CustomizingChadoAdapter">customizing the
Chado adapter</a>.
-<h3><a NAME="ReadingGFF"></a>Reading Ensembl GFF files</h3>
+</p><h3><a name="ReadingGFF"></a>Reading Ensembl GFF files</h3>
<a href="http://www.sanger.ac.uk/Software/formats/GFF">GFF</a> format is
a simple format for transferring genomic annotations. A version of GFF (Ensembl GFF) is used at the
Sanger Institute for storing the human annotations.
-<P>
+<p>
To read in an Ensembl GFF file, choose the "Ensembl GFF" option from the data adapter menu.
You can type your GFF file name in the text box or press the Browse
button to bring up a file chooser. You can also enter a FASTA-format
@@ -484,40 +492,60 @@
When you're ready, press the OK button and the GFF file (and sequence file, if
you specified one)
will be read in and the features displayed.
-<P>
-<center><img SRC="images/gff-adapter.gif" width=605 height=270></center>
-<P>If any of the features in the GFF file have types that are not recognized
+</p><p>
+</p><center><img src="images/gff-adapter.gif" height="270" width="605"></center>
+<p>If any of the features in the GFF file have types that are not recognized
by Apollo they will be given a default pale yellow color.
-This can be changed in the <a href="#Preferences">Preferences</a>section.
-<P>
+This can be changed in the <a href="#Preferences">Preferences</a> section or by right-clicking over the appropriate feature box in the <a href="#TypesPanel">Types panel</a>.
+</p><p>
Please note that there is more than one flavor of GFF, and Apollo only supports
-the Ensembl flavor (as described <a href=http://www.sanger.ac.uk/Software/formats/GFF>here</a>).
+the Ensembl flavor (as described <a href="http://www.sanger.ac.uk/Software/formats/GFF">here</a>).
Apollo does <i>not</i> understand the Artemis flavor of GFF.
-<P>
+</p><p>
Also note that Ensembl GFF format is not rich enough to support curated annotation, so even if you turn
on editing, you will not be able to create and save curated annotations on GFF-format data.
-<P>
+</p><p>
Finally, note that although theoretically Apollo can be used to convert between data formats
(e.g. GFF <-> GAME), in practice this is not foolproof.
-<h3><a NAME="ReadingGFF3"></a>Reading GFF3 files</h3>
+</p><h3><a name="ReadingGFF3"></a>Reading GFF3 files</h3>
<a href="http://www.sequenceontology.org/gff3.shtml">GFF3</a> format is
-the current generation of a simple format for transferring genomic annotations. <P>
-To read in an GFF3 file, choose the "GFF3 format" option from the data adapter menu. You can type your GFF3 file name in the text box or press the Browse button to bring up a file chooser. You must either provide the sequence data in FASTA format or you will need to have the FASTA data embedded in the GFF3 file. For the first option, make sure that "Embedded FASTA in GFF" is not checked and enter the FASTA file to go with the GFF3 data (you can browse for the file as well). For the second option, make sure that "Embedded FASTA in GFF" is checked. This will disable the "Sequence file" selection. When you're ready, press the OK button and the GFF3 file and sequence data will be read in and the features displayed.
-<P>
-<center><img SRC="images/gff3-adapter.gif" width=605 height=271></center>
-<P>If any of the features in the GFF3 file have types that are not recognized
+the current generation of a simple format for transferring genomic annotations. <p>
+To read in an GFF3 file, choose the "GFF3 format" option from the data
+adapter menu. You can type your GFF3 file name in the text box or press
+ the Browse button to bring up a file chooser. You must either provide
+the sequence data in FASTA format or you will need to have the FASTA
+data embedded in the GFF3 file. For the first option, make sure that
+"Embedded FASTA in GFF" is not checked and enter the FASTA file to go
+with the GFF3 data (you can browse for the file as well). For the
+second option, make sure that "Embedded FASTA in GFF" is checked. This
+will disable the "Sequence file" selection. When you're ready, press
+the OK button and the GFF3 file and sequence data will be read in and
+the features displayed.
+</p><p>
+</p><center><img src="images/gff3-adapter.gif" height="271" width="605"></center>
+<p>If any of the features in the GFF3 file have types that are not recognized
by Apollo they will be given a default pale yellow color.
-This can be changed in the <a href="#Preferences">Preferences</a>section.
-<P>
+This can be changed in the <a href="#Preferences">Preferences</a> section or by right-clicking over the appropriate feature box
+in the <a href="#TypesPanel">Types panel</a>.
+</p><p>
-<h3><a name="Reading_Ensembl_via_ensj"></a>Reading Ensembl schema databases</h3>
-
-The Ensembl project has created public MySQL databases of annotated genomes for many species - at time of writing this list includes human, mouse, mosquito, rat, zebrafish, and fugu. Each species is stored in a separate, publicly accessible database. The Ensembl adapter can read these databases, as well as any other ensembl-schema MySQL database. The Ensembl project's databases are at ensembldb.sanger.ac.uk, port 3306, accessible as user "anonymous".
-<P>
-To directly read Ensembl databases, use the File->Open menu as usual, and choose "EnsJ - Direct Access for Ensembl Databases (Schema 32 and above)" from the pulldown (note that it may freeze up briefly as it sets up its configuration).
-<P>
+</p><h3><a name="Reading_Ensembl_via_ensj"></a>Reading Ensembl schema databases</h3>
+<p>
+The Ensembl project has created public MySQL databases of annotated
+genomes for many species - at time of writing this list includes human,
+ mouse, mosquito, rat, zebrafish, and fugu. Each species is stored in a
+ separate, publicly accessible database. The Ensembl adapter can read
+these databases, as well as any other ensembl-schema MySQL database. The
+ Ensembl project's databases are at ensembldb.sanger.ac.uk, port 3306,
+accessible as user "anonymous".
+</p><p>
+To directly read Ensembl databases, use the File->Open menu as usual,
+ and choose "EnsJ - Direct Access for Ensembl Databases (Schema 32 and
+ above)" from the pulldown (note that it may freeze up briefly as it
+sets up its configuration).
+</p><p>
The EnsJ adapter is initially set to retrieve data from the Homo sapiens
database at the ensembldb site, but because the database name changes frequently,
the name that is hardcoded in the default Apollo history may no longer be valid.
@@ -525,46 +553,71 @@
(.apollo/apollo.history) and restarting Apollo. Note that the list of
databases may include some with schemas prior to the current one; if you
try to read data from those, you will probably get an inscrutable error message.
-<P>
-After selecting a database (if the default one didn't work), you can select a region
+</p><p>
+After selecting a database (if the default one didn't work), you can
+select a region
to look at.
The "Location" menu allows you to choose a specific gene to view:
either by stable id (e.g. "ENSG00000187981"),
-or by specifying a region of the chromosome (e.g. "Coordinate System: Chromosome (Version NCBI 35), SeqRegion: Chromosome 6, from 500,000 to 1,000,000"--choose "chromosome--NCBI35" for the coordinate system, "6" for the seq region name, and 500000-100000 for start-end).
-<P>
-To try out the EnsJ adapter, click the History pulldown list and select one of the pre-set regions. The relevant fields will be filled in appropriately, so you can just hit "Ok" at the bottom of the window to load the data.
-<P><center><img SRC="images/ensj20_location.gif" width=462 height=419></center><P>
+or by specifying a region of the chromosome (e.g. "Coordinate System:
+Chromosome (Version NCBI 35), SeqRegion: Chromosome 6, from 500,000 to
+1,000,000"--choose "chromosome--NCBI35" for the coordinate system, "6"
+for the seq region name, and 500000-100000 for start-end).
+</p><p>
+To try out the EnsJ adapter, click the History pulldown list and select
+one of the pre-set regions. The relevant fields will be filled in
+appropriately, so you can just hit "Ok" at the bottom of the window to
+load the data.
+</p><p></p><center><img src="images/ensj20_location.gif" height="419" width="462"></center><p>
Note that if you already had run a previous version of Apollo and thus
have an apollo.history file in your .apollo directory, the pre-set EnsJ examples
may not work right. You can fix this by removing .apollo/apollo.history (so that
the new default history takes its place) or by filling in the spaces in the Data
Source panel by hand (see the next subsection).
-<P>
-Ensembl features are categorised into various types. In order to see any of these types in the region you loaded, you must expand the "Types" panel by pushing the "Show/Hide Types" button. You will see the following:
-<P><center><img SRC="images/ensj20_types.gif" width= height=></center><P>
-The numbers beside each type (e.g., Genes (34270)) are the number of features of that type in the whole Ensembl database. Select the types of features you want to see ("Genes" is a good starting point). You must select something from this panel. At this point you should be ready to read data with the default data source configuration (human data at the public servers on ensembldb). You can hit the "OK" button on the dialog, and Apollo will bring up the selected annotations in your chosen region.
-<P>
-The "Types" button beside each feature type (eg "Gene Types...") will show a list of the different types of genes in the Ensembl database. For instance, in the homo sapiens database, there are many types such as protein_coding_KNOWN_ensembl and pseudogene_NOVEL_ensembl.
-These types can be loaded individually by selecting them from this list which is sorted alphabetically. If no types are selected, all types will be loaded.
+</p><p>
+Ensembl features are categorized into various types. In order to see any
+ of these types in the region you loaded, you must expand the "Types"
+panel by pushing the "Show/Hide Types" button. You will see the
+following:
+</p><p></p><center><img src="images/ensj20_types.gif" width="height="></center><p>
+The numbers beside each type (e.g., Genes (34270)) are the number of
+features of that type in the whole Ensembl database. Select the types of
+ features you want to see ("Genes" is a good starting point). You must
+select something from this panel. At this point you should be ready to
+read data with the default data source configuration (human data at the
+ public servers on ensembldb). You can hit the "OK" button on the
+dialog, and Apollo will bring up the selected annotations in your
+chosen region.
+</p><p>
+The "Types" button beside each feature type (eg "Gene Types...") will
+show a list of the different types of genes in the Ensembl database. For
+ instance, in the homo sapiens database, there are many types such as
+protein_coding_KNOWN_ensembl and pseudogene_NOVEL_ensembl.
+These types can be loaded individually by selecting them from this list
+which is sorted alphabetically. If no types are selected, all types will
+ be loaded.
-<h4>Data Source Configurations</h4>
+</p><h4>Data Source Configurations</h4>
The Databases panel specifies where the ensembl database lives, and how
to access it. We have set it up with some defaults, which should
allow you to read human data "out of the box", but you might want to
read ensembl data from some other species, or set up your own ensembl
databases.
-<P>
-<P><center><img SRC="images/ensj20_database_config.gif" width= height=></center><P>
-<P>
-<b>Host</b>: The name of the host on which the ensembl databases live. The publicly accessible site (ensembldb.sanger.ac.uk) is defaulted in this field. If you set up your own ensembl database, or can see another ensembl database nearby, then you will change this field.
-<BR>
+<p>
+</p><p></p><center><img src="images/ensj20_database_config.gif" width="height="></center><p>
+</p><p>
+<b>Host</b>: The name of the host on which the ensembl databases live.
+The publicly accessible site (ensembldb.sanger.ac.uk) is defaulted in
+this field. If you set up your own ensembl database, or can see another
+ ensembl database nearby, then you will change this field.
+<br>
<b>Port</b>: The port on which the database is "listening" for requests. For MySQL, this port is 3306 by default.
-<BR>
+<br>
<b>User</b>: Who Apollo should log in as. The databases on ensembldb all have "anonymous" as the user.
-<BR>
+<br>
<b>Password</b>: The public ensembl databases on ensembldb have no password for the user "anonymous", so you can leave this field blank.
-<BR>
+<br>
<b>Ensembl Database Name</b>: This dropdown is only populated when you
attempt to open it. It shows all the ensembl databases available on the
@@ -572,32 +625,31 @@
field appropriate to the value of the "Data Source" dropdown. We have
defaulted the database to the current human core database
("homo_sapiens_core_32_35e" at time of writing).
-<P>
+</p><p>
Please note: the set of available ensembl databases is constantly changing,
and your history may include databases that are no longer available, which
can make the EnsJ adapter refuse to come up. If this seems to be happening
to you, remove your ~/.apollo/apollo.history and try restarting Apollo.
-<h4>Loading and saving manual annotations - otter format</h4>
+</p><h4>Loading and saving manual annotations - otter format</h4>
This functionality is still being redeveloped for the new EnsJ adapter.
<h3>Reading cross-species comparative data</h3>
-The still-under-development <a href=game-synteny.html>Synteny</a> viewer in Apollo lets you view comparative
+The still-under-development <a href="http://apollo.berkeleybop.org/current/game-synteny.html">Synteny</a> viewer in Apollo lets you view comparative
analyses between two genomes. There are several ways to read synteny data;
currently, the default is GAME synteny, for which a pair of example files
has been included with the Apollo distribution.
-Please see the <a href=game-synteny.html>GAME Synteny user guide</a>
+Please see the <a href="http://apollo.berkeleybop.org/current/game-synteny.html">GAME Synteny user guide</a>
for more information.
-<h3><a NAME="ReadingGenbank"></a>Reading GenBank or EMBL format</h3>
+<h3><a name="ReadingGenbank"></a>Reading GenBank or EMBL format</h3>
Apollo can now read GenBank and EMBL format from files or directly
over the network (given an accession number). GenBank format looks like this:
-<P>
-<pre>
-LOCUS AY308719 1036 bp DNA linear VRT 31-MAY-2004
+<p>
+</p><pre>LOCUS AY308719 1036 bp DNA linear VRT 31-MAY-2004
DEFINITION Parus elegans mindanensis FMNH 357569 cytochrome b gene, partial
cds; mitochondrial gene for mitochondrial product.
ACCESSION AY308719
@@ -606,27 +658,25 @@
source 1..1036
/organism="Parus elegans mindanensis"
</pre>
-<P>
-EMBL format looks like this:<P>
-<pre>
-ID DME9736 standard; genomic DNA; INV; 7411 BP.
+<p>
+EMBL format looks like this:</p><p>
+</p><pre>ID DME9736 standard; genomic DNA; INV; 7411 BP.
XX
AC AJ009736;
</pre>
-<P>
+<p>
We are still working on this adapter. In particular, reading as GenBank
or EMBL and then saving in GenBank format doesn't perfectly preserve
everything from the original source.
-<P>
+</p><p>
When you save in GenBank format, you have a choice of saving in a normal
-human-readable GenBank file (as in the example above) or in <a target=_new href=
-http://www.ncbi.nlm.nih.gov/Sequin/table.html>tabular format</a>,
+human-readable GenBank file (as in the example above) or in <a target="_new" href="http://www.ncbi.nlm.nih.gov/Sequin/table.html">tabular format</a>,
which is mostly used for submitting data to GenBank. If you want to save in
tabular format, you must supply a <i>directory</i> name, not a file name;
multiple files will be saved in the directory. To save in human-readable
GenBank format, supply a file name.
-<h3><a NAME="AnalysisAdapter"></a>Reading raw analysis results</h3>
+</p><h3><a name="AnalysisAdapter"></a>Reading raw analysis results</h3>
The analysis adapter (called "Computational analysis results" in the data
loader menu) is one of the newest additions to Apollo; it still is in
@@ -638,34 +688,34 @@
format. (However, keep in mind that you are responsible for running
your own sequence analyses--Apollo does not and will not act as a "back end"
and run the analyses itself, because they are too system-dependent.)
-<P>
+<p>
Different tabs in the analysis adapter allow you to import various types of analysis results on your sequence:
-<UL>
-<LI> BLAST<BR>
-<LI> sim4<BR>
-<LI> blat<BR>
-<LI> FgenesH<BR>
-<LI> Genscan<BR>
-<LI> tRNAscanSE<BR>
-<LI> RepeatMasker
-</UL>
+</p><ul>
+<li> BLAST<br>
+</li><li> sim4<br>
+</li><li> blat<br>
+</li><li> FgenesH<br>
+</li><li> Genscan<br>
+</li><li> tRNAscanSE<br>
+</li><li> RepeatMasker
+</li></ul>
Each one lets you specify a FASTA file containing the genomic query sequence
that was used in the sequence analysis, and the tier and type to be used for
displaying the data in Apollo. Some of the analysis tabs offer filtering/processing
options, such as the minimum threshold for including BLAST hits.
-<P>
+<p>
At the moment, many of the analysis parsers are not working right.
Some of the sequence analysis programs, such as BLAT, seem to have
changed their output format since the Apollo parsers were written.
The BLAST and Genscan parsers seem to be the best ones right now.
Stay tuned for more documentation and improved performance. In the meantime,
if you have questions about the analysis adapter, please contact the
-<a href=#mailing>Apollo mailing list</a>.
-<P>
+<a href="#mailing">Apollo mailing list</a>.
+</p><p>
The BLAST parser offers many filtering options. In most cases, you can just
leave those alone. We hope in the future to reduce the complexity of the options.
-<h4>Loading BLASTN results</h4>
+</p><h4>Loading BLASTN results</h4>
There are many different variations of BLAST format. The two main flavors of BLAST
are NCBI BLAST and WU-BLAST. Theoretically, Apollo's BLAST parser should figure
@@ -673,9 +723,9 @@
minor variations in BLAST output syntax can cause the parser to fail. As of August 2005,
the parser seems to be working pretty well on NCBI BLASTN 2.2.11 output from the NCBI
blast server
-(<a target=_new href=http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=chromosome&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=Text&NCBI_GI=on&PAGE=Nucleotides&PROGRAM=blastn&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS.y=8&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes>http://www.ncbi.nlm.nih.gov/blast/Blast.cgi</a>).
+(<a target="_new" href="http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATABASE=chromosome&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=10&FILTER=L&FORMAT_OBJECT=Alignment&FORMAT_TYPE=Text&NCBI_GI=on&PAGE=Nucleotides&PROGRAM=blastn&SERVICE=plain&SET_DEFAULTS.x=34&SET_DEFAULTS.y=8&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes">http://www.ncbi.nlm.nih.gov/blast/Blast.cgi</a>).
(This link is also available on Apollo's Links menu.)
-<P>
+<p>
Select "chromosomes" as the database.
You can select an organism or category of organisms in the Options section.
Be sure the last pulldown list on the first row of the Format section says "Plain text".
@@ -685,7 +735,7 @@
is to select all the BLAST result text in the browser window (some browsers have
"Select all" under the Edit menu), copy it, and paste it into a plain text file (be sure the
lines don't wrap).
-<h3><a NAME="Layering"></a>Layering data</h3>
+</p><h3><a name="Layering"></a>Layering data</h3>
Some of the data adapters are able to "layer" features that are from the
same genomic region. For example, you might have separate files of
@@ -694,26 +744,33 @@
what you've already loaded. This only makes sense if the new data is
from the same genomic region--if it's from a different region, you will
probably get a blank popup error box.
-<P>
+<p>
Another popular use of the layering option is to add new analysis results
for the current region--for example, maybe you BLASTed the currently displayed genomic
sequence against a new database, and want to see the results displayed along
with the other evidence. To do this, use the "Layer more results or annotations"
command from the File menu, and choose the "Computational analysis results"
data loader from the pulldown list under "Choose data source".
-<P>
+</p><p>
If you are preparing your own data files for layering, please note that
you must identify the genomic region (e.g. chromosome arm) in each file (even if you don't include
the sequence residues), so that Apollo knows where the features go.
-<P>
-The most common scenario for layering BLAST results is that you've already loaded
-the annotations for some genomic region (say, D. melanogaster 2L:12345-67890); you
-then BLASTN an EST against the D. melanogaster chromosomes (see the section on Loading BLASTN results above), and you want to see
-where it matches your currently loaded region. To do this, use the "Computational analysis
-results" data adapter, and select the BLAST tab. The checkbox that says "I used
-the current genomic sequence (or a portion thereof) as my BLAST query" should
-remain unchecked (the default) and you will not need to enter a genomic offset.
-<P><center><img SRC="images/layer-blast.gif"></center><P>
+</p><p>
+The most common scenario for layering BLAST results is that you've
+already loaded
+the annotations for some genomic region (say, D. melanogaster
+2L:12345-67890); you
+then BLASTN an EST against the D. melanogaster chromosomes (see the
+section on Loading BLASTN results above), and you want to see
+where it matches your currently loaded region. To do this, use the
+"Computational analysis
+results" data adapter, and select the BLAST tab. The checkbox that says
+ "I used
+the current genomic sequence (or a portion thereof) as my BLAST query"
+should
+remain unchecked (the default) and you will not need to enter a genomic
+offset.
+</p><p></p><center><img src="images/layer-blast.gif"></center><p>
When you load your BLAST results, Apollo will display
only the hits against the currently loaded chromosome or chromosome arm (but some
of them may be to a different region of the chromosome). This capability is still
@@ -723,20 +780,24 @@
that BLAST assumes all query sequences are on the + strand--it doesn't have a
notion of a query sequence being on the - strand. The hits will therefore all
show up relative to the + strand of the current region.
-<P>
+</p><p>
Another thing to be aware of (unless this has been fixed recently) is that the
chromosome coordinates on the D. melanogaster data from FlyBase don't match
the coordinates from NCBI, so if you load a Drosophila region and try to layer
NCBI BLAST hits, they will not show up in the right place--they'll appear
somewhat shifted to the 3' end. This is a data problem, not an Apollo bug,
though there are very likely bugs in Apollo's BLAST parser as well.
-<P>
+</p><p>
If you BLASTed some or all of the current genomic sequence against a
-database at NCBI, you should check off "I used the current genomic sequence
-(or a portion thereof) as my BLAST query." If you used only a portion of
-the current genomic sequence, enter the offset of the sequence you used from the starting position of the current genomic region (we plan to automate this offset calculation soon).
+database at NCBI, you should check off "I used the current genomic
+sequence
+(or a portion thereof) as my BLAST query." If you used only a portion
+of
+the current genomic sequence, enter the offset of the sequence you used
+from the starting position of the current genomic region (we plan to
+automate this offset calculation soon).
-<h2><a NAME="CommandLine"></a>Launching Apollo with command-line arguments</h2>
+</p><h2><a name="CommandLine"></a>Launching Apollo with command-line arguments</h2>
Unix users can launch Apollo on a datafile by using the appropriate command-line arguments. Use "--help"
to get a list of the options. Valid arguments are:
<pre>
@@ -779,27 +840,30 @@
files into a DB (chado)
-? (or --help) Show this help message
</pre>
-The command-line arguments changed starting with release 1.5.0, but for now
-most of the older command-line arguments (e....
[truncated message content] |
|
From: Suzanna L. <su...@be...> - 2010-10-11 14:03:06
|
I'm checking up on this. We did just retire the old fruitfly mail server. Seth and/or Nomi and/or Ed. Would you chime in please. On Oct 11, 2010, at 2:29 AM, Rob Syme wrote: > The Apollo mailing list url > (http://mail.fruitfly.org/mailman/listinfo/apollo) listed: > http://apollo.berkeleybop.org/current/userguide.html#mailing > and > http://gmod.org/wiki/Apollo#Mailing_Lists > > seems to be no longer available. Is there a mailing list for Apollo > users (not devs)? I am troubleshooting a Chado/Apollo connection. > -r > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Gmod-apollo-cmts mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-apollo-cmts |
|
From: Rob S. <rob...@gm...> - 2010-10-11 06:30:12
|
The Apollo mailing list url (http://mail.fruitfly.org/mailman/listinfo/apollo) listed: http://apollo.berkeleybop.org/current/userguide.html#mailing and http://gmod.org/wiki/Apollo#Mailing_Lists seems to be no longer available. Is there a mailing list for Apollo users (not devs)? I am troubleshooting a Chado/Apollo connection. -r |
|
From: <no...@us...> - 2010-07-02 18:39:36
|
Revision: 23526
http://gmod.svn.sourceforge.net/gmod/?rev=23526&view=rev
Author: nomi
Date: 2010-07-02 18:39:28 +0000 (Fri, 02 Jul 2010)
Log Message:
-----------
Fixed instructions for downloading and compiling Apollo code.
Modified Paths:
--------------
apollo/trunk/doc/html/userguide.html
Modified: apollo/trunk/doc/html/userguide.html
===================================================================
--- apollo/trunk/doc/html/userguide.html 2010-07-02 17:48:42 UTC (rev 23525)
+++ apollo/trunk/doc/html/userguide.html 2010-07-02 18:39:28 UTC (rev 23526)
@@ -3628,51 +3628,34 @@
<h2>Getting the source code</h2>
<a NAME="source"></a>
You can download the latest Apollo source code from
-<a href=http://sourceforge.net/projects/gmod>SourceForge</a>. Each major release includes a
-<a href=http://sourceforge.net/project/showfiles.php?group_id=27707>tarfile of the
-SourceForge</a>. If you are going to be actively involved in changing the Apollo code, though, you are better off getting the up-to-the-minute code from <a href=http://sourceforge.net/cvs/?group_id=27707>
-SourceForge CVS</a>.
+<a href=http://sourceforge.net/projects/gmod/files/>SourceForge</a>. Each
+major release is available as a gzipped tar file. If you are going to be
+actively involved in changing the Apollo code, though, you are better off
+getting the up-to-the-minute code
+from the <a href=http://gmod.svn.sourceforge.net/viewvc/gmod/apollo/>
+SourceForge SVN repository</a>.
<P>
-Here is the command you can use for checking out the whole Apollo
-distribution from sourceforge:
+To check out the whole Apollo distribution from SourceForge, say:
<pre>
-setenv CVS_RSH ssh
-cvs -z3 -d:ext:mya...@gm...:/cvsroot/gmod checkout -d apollo apollo
+svn co https://gmod.svn.sourceforge.net/svnroot/gmod/apollo/trunk apollo
</pre>
-For "myaccount", substitute your own SourceForge account name. (It's a good
-idea to get a SourceForge account if you're going to be doing this--it's
-quick, free, and they don't send you spam.) If you don't want to get an
-account on SourceForge, you can do an anonymous checkout; however,
-anonymous checkouts give you a version that's a few days out of date.
-To check out an anonymous version:
-<pre>
-cvs -d:pserver:ano...@gm...:/cvsroot/gmod login
-cvs -d:pserver:ano...@gm...:/cvsroot/gmod checkout -d apollo apollo
-</pre>
<P>
-The "-d apollo" specifies the directory name you want the Apollo stuff to
-go in, so you can change that if you want to put it somewhere else.
-<P>
-After you've checked out the code, compiling it is straightforward:
+After you've checked out the distribution, you will need <a target=ant href=http://ant.apache.org/>Ant</a> (available free
+from http://ant.apache.org/) to
+compile the source. Then do the following:
<pre>
cd apollo
-setenv APOLLO_ROOT `pwd`
+setenv APOLLO_ROOT `pwd` [or APOLLO_ROOT=`pwd` if you use bash]
cd src/java
-make clean [only necessary if you've already compiled and then updated]
-make jar
+ant jar
</pre>
-You can also use <a target=ant href=http://ant.apache.org/>Ant</a> (available free
-from http://ant.apache.org/) to
-compile the source. It runs faster than make and is also easier to use if
-you're working on a Windows platform.
<P>
To run your newly compiled apollo say:
<pre>
~/apollo/bin/apollo
</pre>
(where ~/apollo is the directory where you've installed apollo--change
-as appropriate). You won't be able to run "Apollo" (with a capital A) like
-you may have done if you used the installed version of Apollo.
+as appropriate).
<P>
Note that all these instructions assume that you're on a Unix-y
system. If you're on Windows and you've already installed Apollo, you
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <no...@us...> - 2010-07-02 16:59:04
|
Revision: 23522
http://gmod.svn.sourceforge.net/gmod/?rev=23522&view=rev
Author: nomi
Date: 2010-07-02 16:58:47 +0000 (Fri, 02 Jul 2010)
Log Message:
-----------
Replaced out-of-date URLs for Apollo with current ones
Modified Paths:
--------------
apollo/trunk/README
Modified: apollo/trunk/README
===================================================================
--- apollo/trunk/README 2010-07-01 18:40:07 UTC (rev 23521)
+++ apollo/trunk/README 2010-07-02 16:58:47 UTC (rev 23522)
@@ -5,9 +5,10 @@
levels of detail, and to perform expert annotation curation, all in a
graphical environment.
-This distribution is intended mostly for developers - it does not include
-the installer. If you'd like to install Apollo on your Mac or Windows
-machine, please visit http://www.fruitfly.org/annot/apollo/install.html.
+This distribution is intended mostly for developers - it does not include the
+installer. If you'd like to install Apollo on your Mac or Windows or Linux
+machine, please visit http://apollo.berkeleybop.org/current/install.html.
For more developer information, see the README files in doc/. For user
-documentation see doc/html/userguide.html or go to http://fruitfly.org/apollo.
+documentation, see doc/html/userguide.html or go to
+http://apollo.berkeleybop.org/.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gk...@us...> - 2010-05-12 21:22:01
|
Revision: 23189
http://gmod.svn.sourceforge.net/gmod/?rev=23189&view=rev
Author: gk_fan
Date: 2010-05-12 21:21:51 +0000 (Wed, 12 May 2010)
Log Message:
-----------
GFF3Adapter now skip CDS features that lack a "Parent" attribute (rather than crashing).
Modified Paths:
--------------
apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-05-12 21:19:09 UTC (rev 23188)
+++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-05-12 21:21:51 UTC (rev 23189)
@@ -896,7 +896,12 @@
private void processCds(GFF3Entry entry, Map<String, int[]> cdsCoords)
{
- for (String pid : entry.getAttributeValues("Parent")) {
+ List<String> parents = entry.getAttributeValues("Parent");
+ if (parents == null) {
+ logger.warn("No Parent attribute for CDS " + entry.getId());
+ return;
+ }
+ for (String pid : parents) {
int []coords = cdsCoords.get(pid);
if (coords == null) {
coords = new int[] {entry.getStart(), entry.getEnd()};
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <gk...@us...> - 2010-05-12 21:19:29
|
Revision: 23188
http://gmod.svn.sourceforge.net/gmod/?rev=23188&view=rev
Author: gk_fan
Date: 2010-05-12 21:19:09 +0000 (Wed, 12 May 2010)
Log Message:
-----------
Fixed infinite loop when calculating scoring factor when it encounters a score of 0.
Modified Paths:
--------------
apollo/trunk/src/java/apollo/gui/WiggleScoreCalculator.java
Modified: apollo/trunk/src/java/apollo/gui/WiggleScoreCalculator.java
===================================================================
--- apollo/trunk/src/java/apollo/gui/WiggleScoreCalculator.java 2010-05-12 20:04:00 UTC (rev 23187)
+++ apollo/trunk/src/java/apollo/gui/WiggleScoreCalculator.java 2010-05-12 21:19:09 UTC (rev 23188)
@@ -143,7 +143,7 @@
else {
continue;
}
- if (Math.abs(score) < minAbsScore) {
+ if (score != 0 && Math.abs(score) < minAbsScore) {
minAbsScore = Math.abs(score);
}
for (int i = pos; i <= pos + span; ++i) {
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|
|
From: <gk...@us...> - 2010-05-05 14:17:05
|
Revision: 23134
http://gmod.svn.sourceforge.net/gmod/?rev=23134&view=rev
Author: gk_fan
Date: 2010-05-05 14:16:49 +0000 (Wed, 05 May 2010)
Log Message:
-----------
+ Fixed GFF3 input from URL when run from the command line
Modified Paths:
--------------
apollo/trunk/src/java/apollo/dataadapter/DataInput.java
apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
Modified: apollo/trunk/src/java/apollo/dataadapter/DataInput.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/DataInput.java 2010-05-05 13:26:27 UTC (rev 23133)
+++ apollo/trunk/src/java/apollo/dataadapter/DataInput.java 2010-05-05 14:16:49 UTC (rev 23134)
@@ -124,14 +124,27 @@
return getInputString() != null;
}
- public boolean isFile() { return getType() == DataInputType.FILE; }
-
+ public boolean isFile() {
+ return getType() == DataInputType.FILE;
+ }
+
public String getFilename() {
if (!isFile())
return null;
return getInputString();
}
+
+ public boolean isUrl() {
+ return getType() == DataInputType.URL;
+ }
+ public String getUrl() {
+ if (!isUrl()) {
+ return null;
+ }
+ return getInputString();
+ }
+
/** Returns true if DataInputType is BASEPAIR_RANGE */
public boolean isRegion() {
return getType() == DataInputType.BASEPAIR_RANGE;
Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-05-05 13:26:27 UTC (rev 23133)
+++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-05-05 14:16:49 UTC (rev 23134)
@@ -122,7 +122,12 @@
*/
public void setDataInput(apollo.dataadapter.DataInput di)
{
- setGffFilename(di.getFilename());
+ if (di.isFile()) {
+ setGffFilename(di.getFilename());
+ }
+ else if (di.isUrl()) {
+ setGffFilename(di.getUrl());
+ }
if (di.hasSequenceFilename()) {
setSeqFilename(di.getSequenceFilename());
}
@@ -238,6 +243,7 @@
*/
private void writeSeqs(PrintWriter out, List<SequenceI> seqs)
{
+ out.println("##FASTA");
for (SequenceI seq : seqs) {
if (seq.getLength() > 0) {
out.print(FastaFile.print(seq));
@@ -597,169 +603,168 @@
Map<String, int []> cdsCoords, CurationSet curation)
throws ApolloAdapterException
{
- Map<String, FeatureSetI[]> resultSets =
- new TreeMap<String, FeatureSetI[]>();
- Set<String> errors = new HashSet<String>();
- Set<GFF3Data> matches = new HashSet<GFF3Data>();
- for (Map.Entry<String, GFF3Data> mapEntry : gffMap.entrySet()) {
- GFF3Data data = mapEntry.getValue();
- GFF3Entry gff = data.getEntry();
- SeqFeatureI feat = data.getFeat();
- feat.setRefSequence(curation.getRefSequence());
- if (!gff.isAnnotation()) {
- processEvidence(feat);
- }
- // add matches for post processing if they're missing match_part features
- if (gff.getType().equals("match")) {
- matches.add(data);
- }
- boolean added = false;
- List<String> pids = gff.getAttributeValues("Parent");
- if (pids != null) {
- int pnum = 0;
- for (String pid : pids) {
- GFF3Data pdata = gffMap.get(pid);
- if (gff.isAnnotation()) {
- SeqFeatureI parent = pdata.getFeat();
- if (!feat.isTranscript() && !feat.isExon()) {
- if (!errors.contains(feat.getName())) {
- IOUtil.errorDialog("Only transcripts and exons can be children of annotations: " +
- feat.getName() + "[" + feat.getFeatureType() + "]");
- errors.add(feat.getName());
- }
- added = true;
- continue;
+ Map<String, FeatureSetI[]> resultSets = new TreeMap<String, FeatureSetI[]>();
+ Set<String> errors = new HashSet<String>();
+ Set<GFF3Data> matches = new HashSet<GFF3Data>();
+ for (Map.Entry<String, GFF3Data> mapEntry : gffMap.entrySet()) {
+ GFF3Data data = mapEntry.getValue();
+ GFF3Entry gff = data.getEntry();
+ SeqFeatureI feat = data.getFeat();
+ feat.setRefSequence(curation.getRefSequence());
+ if (!gff.isAnnotation()) {
+ processEvidence(feat);
+ }
+ // add matches for post processing if they're missing match_part features
+ if (gff.getType().equals("match")) {
+ matches.add(data);
+ }
+ boolean added = false;
+ List<String> pids = gff.getAttributeValues("Parent");
+ if (pids != null) {
+ int pnum = 0;
+ for (String pid : pids) {
+ GFF3Data pdata = gffMap.get(pid);
+ if (gff.isAnnotation()) {
+ SeqFeatureI parent = pdata.getFeat();
+ if (!feat.isTranscript() && !feat.isExon()) {
+ if (!errors.contains(feat.getName())) {
+ IOUtil.errorDialog("Only transcripts and exons can be children of annotations: " +
+ feat.getName() + "[" + feat.getFeatureType() + "]");
+ errors.add(feat.getName());
}
- if (feat.isExon() && !parent.isTranscript()) {
- if (!errors.contains(feat.getName())) {
- IOUtil.errorDialog("Exons can only be children of transcripts: " + feat.getName() + " -> " +
- parent.getName() + "[" + parent.getFeatureType() + "]");
- errors.add(feat.getName());
- }
- added = true;
- continue;
- }
- }
- ++pnum;
- if (pdata == null) { //orphan
- logger.warn("Missing parent " + pid + " for " +
- gff.getName());
+ added = true;
continue;
}
- if (pnum > 1) {
- if (pnum == 2) {
- feat.setId(feat.getId() + "-1");
+ if (feat.isExon() && !parent.isTranscript()) {
+ if (!errors.contains(feat.getName())) {
+ IOUtil.errorDialog("Exons can only be children of transcripts: " + feat.getName() + " -> " +
+ parent.getName() + "[" + parent.getFeatureType() + "]");
+ errors.add(feat.getName());
}
- feat = feat.cloneFeature();
- feat.setId(feat.getId().replaceFirst("-\\d+$",
- "-" + pnum));
+ added = true;
+ continue;
}
- if (gff.isAnnotation()) {
- processAnnotation(data, pdata.getFeat(), cdsCoords);
+ }
+ ++pnum;
+ if (pdata == null) { //orphan
+ logger.warn("Missing parent " + pid + " for " +
+ gff.getName());
+ continue;
+ }
+ if (pnum > 1) {
+ if (pnum == 2) {
+ feat.setId(feat.getId() + "-1");
}
- try {
- pdata.getFeat().addFeature(feat);
- added = true;
- }
- catch (ClassCastException e) {
- /*
+ feat = feat.cloneFeature();
+ feat.setId(feat.getId().replaceFirst("-\\d+$",
+ "-" + pnum));
+ }
+ if (gff.isAnnotation()) {
+ processAnnotation(data, pdata.getFeat(), cdsCoords);
+ }
+ try {
+ pdata.getFeat().addFeature(feat);
+ added = true;
+ }
+ catch (ClassCastException e) {
+ /*
throw new ApolloAdapterException("Cannot add " + feat +
"(" + data.getEntry().getType() + ")" + " to " +
pdata.getFeat() + "(" + pdata.getEntry().getType() +
")");
- */
- logger.warn("Cannot add " + feat +
- "(" + data.getEntry().getType() + ")" + " to " +
- pdata.getFeat() + "(" + pdata.getEntry().getType() +
- ")");
- }
+ */
+ logger.warn("Cannot add " + feat +
+ "(" + data.getEntry().getType() + ")" + " to " +
+ pdata.getFeat() + "(" + pdata.getEntry().getType() +
+ ")");
}
}
- //a transcript can potentially not have a gene associated with it, in which
- //case we need to generate one (the GFF3 spec doesn't REQUIRE a transcript
- //to have a gene, which seems kind of silly to me...)
- else {
- if (!feat.isAnnotTop()) {
- if (gff.isAnnotation()) {
- logger.warn("No parent feature found for " + feat +
- "(" + gff.getType() + "). Generating dummy parent feature.");
- generateParent(feat, annots);
- added = true;
- }
+ }
+ //a transcript can potentially not have a gene associated with it, in which
+ //case we need to generate one (the GFF3 spec doesn't REQUIRE a transcript
+ //to have a gene, which seems kind of silly to me...)
+ else {
+ if (!feat.isAnnotTop()) {
+ if (gff.isAnnotation()) {
+ logger.warn("No parent feature found for " + feat +
+ "(" + gff.getType() + "). Generating dummy parent feature.");
+ generateParent(feat, annots);
+ added = true;
}
}
- if (!added) {
- if (gff.isAnnotation()) {
- // need to wrap one-level annotations in a AnnotationFeatureI otherwise Apollo isn't happy
- if (feat.isAnnotTop() && gff.isOneLevelAnnotation()) {
- AnnotatedFeatureI fs = new AnnotatedFeature();
- fs.addFeature(feat);
- fs.setStrand(feat.getStrand());
- fs.setId(feat.getId() + "-fs");
- fs.setFeatureType(feat.getFeatureType());
- feat = fs;
- }
- // arbitrarily add strand-less features to plus strand
- if (feat.getStrand() == 0) {
- annots.getForwardSet().addFeature(feat);
- }
- else {
- annots.addFeature(feat);
- }
+ }
+ if (!added) {
+ if (gff.isAnnotation()) {
+ // need to wrap one-level annotations in a AnnotationFeatureI otherwise Apollo isn't happy
+// if (feat.isAnnotTop() && gff.isOneLevelAnnotation()) {
+// AnnotatedFeatureI fs = new AnnotatedFeature();
+// fs.addFeature(feat);
+// fs.setStrand(feat.getStrand());
+// fs.setId(feat.getId() + "-fs");
+// fs.setFeatureType(feat.getFeatureType());
+// feat = fs;
+// }
+ // arbitrarily add strand-less features to plus strand
+ if (feat.getStrand() == 0) {
+ annots.getForwardSet().addFeature(feat);
}
else {
- processEvidence(feat);
- FeatureSetI []fsArray = resultSets.get(gff.getSource());
- if (fsArray == null) {
- fsArray = new FeatureSet[2];
- resultSets.put(gff.getSource(), fsArray);
- }
- int arrayIdx = gff.getStrand() == 1 ? 1 : 0;
- FeatureSetI fs = fsArray[arrayIdx];
- if (fs == null) {
- fs = new FeatureSet(gff.getSource(), gff.getStrand());
- fsArray[arrayIdx] = fs;
- }
- fs.addFeature(feat);
- /*
- results.addFeature(feat);
- */
+ annots.addFeature(feat);
}
}
- }
-
- // add FeaturePair objects to any matches with no match_part children
- for (GFF3Data data : matches) {
- SeqFeatureI match = data.getFeat();
- if (match.getFeatures().size() == 0) {
- GFF3Entry matchPart = new GFF3Entry(data.getEntry().toString());
- matchPart.setType("match_part");
- try {
- SeqFeatureI matchPartFeat = matchPart.createFeature(oboParser);
- processEvidence(matchPartFeat);
- match.addFeature(matchPartFeat);
+ else {
+ processEvidence(feat);
+ FeatureSetI []fsArray = resultSets.get(gff.getSource());
+ if (fsArray == null) {
+ fsArray = new FeatureSet[2];
+ resultSets.put(gff.getSource(), fsArray);
}
- catch (ClassNotFoundException e) {
- throw new ApolloAdapterException("Cannot locate Apollo datamodel class: " + e.getMessage());
+ int arrayIdx = gff.getStrand() == 1 ? 1 : 0;
+ FeatureSetI fs = fsArray[arrayIdx];
+ if (fs == null) {
+ fs = new FeatureSet(gff.getSource(), gff.getStrand());
+ fsArray[arrayIdx] = fs;
}
- catch (IllegalAccessException e) {
- throw new ApolloAdapterException(e);
- }
- catch (InstantiationException e) {
- throw new ApolloAdapterException("Cannot instantiate class: " + e.getMessage());
- }
+ fs.addFeature(feat);
+ /*
+ results.addFeature(feat);
+ */
}
}
+ }
- for (Map.Entry<String, FeatureSetI[]> e : resultSets.entrySet()) {
- if (e.getValue()[0] != null) {
- results.addFeature(e.getValue()[0]);
+ // add FeaturePair objects to any matches with no match_part children
+ for (GFF3Data data : matches) {
+ SeqFeatureI match = data.getFeat();
+ if (match.getFeatures().size() == 0) {
+ GFF3Entry matchPart = new GFF3Entry(data.getEntry().toString());
+ matchPart.setType("match_part");
+ try {
+ SeqFeatureI matchPartFeat = matchPart.createFeature(oboParser);
+ processEvidence(matchPartFeat);
+ match.addFeature(matchPartFeat);
}
- if (e.getValue()[1] != null) {
- results.addFeature(e.getValue()[1]);
+ catch (ClassNotFoundException e) {
+ throw new ApolloAdapterException("Cannot locate Apollo datamodel class: " + e.getMessage());
}
+ catch (IllegalAccessException e) {
+ throw new ApolloAdapterException(e);
+ }
+ catch (InstantiationException e) {
+ throw new ApolloAdapterException("Cannot instantiate class: " + e.getMessage());
+ }
}
- setTranslationEnds(gffMap, cdsCoords);
+ }
+
+ for (Map.Entry<String, FeatureSetI[]> e : resultSets.entrySet()) {
+ if (e.getValue()[0] != null) {
+ results.addFeature(e.getValue()[0]);
+ }
+ if (e.getValue()[1] != null) {
+ results.addFeature(e.getValue()[1]);
+ }
+ }
+ setTranslationEnds(gffMap, cdsCoords);
}
private void generateParent(SeqFeatureI feat, StrandedFeatureSetI annots)
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|
From: <gk...@us...> - 2010-03-11 16:30:19
|
Revision: 22797
http://gmod.svn.sourceforge.net/gmod/?rev=22797&view=rev
Author: gk_fan
Date: 2010-03-11 16:30:11 +0000 (Thu, 11 Mar 2010)
Log Message:
-----------
Fixed wrapping of one level annotations in an AnnotatedFeatureI object to only be done for specific one level annotations (this prevents features like contigs from being displayed).
Modified Paths:
--------------
apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-03-11 16:10:00 UTC (rev 22796)
+++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-03-11 16:30:11 UTC (rev 22797)
@@ -690,12 +690,13 @@
}
if (!added) {
if (gff.isAnnotation()) {
- // need to wrap one-level annotations (non-genes) in a AnnotationFeatureI otherwise Apollo isn't happy
- if (feat.isAnnotTop() && !gff.getType().contains("gene")) {
+ // need to wrap one-level annotations in a AnnotationFeatureI otherwise Apollo isn't happy
+ if (feat.isAnnotTop() && gff.isOneLevelAnnotation()) {
AnnotatedFeatureI fs = new AnnotatedFeature();
fs.addFeature(feat);
fs.setStrand(feat.getStrand());
fs.setId(feat.getId() + "-fs");
+ fs.setFeatureType(feat.getFeatureType());
feat = fs;
}
// arbitrarily add strand-less features to plus strand
@@ -906,7 +907,7 @@
}
}
}
-
+
private Collection<String> getOBOFilenames() throws ApolloAdapterException
{
Style style = getStyle();
@@ -937,7 +938,7 @@
fnames.add(apolloFile);
return fnames;
}
-
+
private class GFF3Data
{
private GFF3Entry entry;
@@ -989,7 +990,7 @@
{
return fname.contains("://");
}
-
+
private static Reader getReader(String fname) throws IOException
{
InputStream is;
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|
|
From: <gk...@us...> - 2010-03-04 18:58:57
|
Revision: 22762
http://gmod.svn.sourceforge.net/gmod/?rev=22762&view=rev
Author: gk_fan
Date: 2010-03-04 18:58:41 +0000 (Thu, 04 Mar 2010)
Log Message:
-----------
Updated to CORRECT version (1.11.4) for release.
Modified Paths:
--------------
apollo/trunk/src/java/apollo/main/Version.java
Modified: apollo/trunk/src/java/apollo/main/Version.java
===================================================================
--- apollo/trunk/src/java/apollo/main/Version.java 2010-03-04 18:56:35 UTC (rev 22761)
+++ apollo/trunk/src/java/apollo/main/Version.java 2010-03-04 18:58:41 UTC (rev 22762)
@@ -7,7 +7,7 @@
*/
public class Version {
- public static String version = "Apollo Genome Annotation and Curation Tool, version 1.11.2";
+ public static String version = "Apollo Genome Annotation and Curation Tool, version 1.11.4";
public static String getVersion() {
String timestamp = Config.getTimestamp();
if (timestamp == null)
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|
|
From: <gk...@us...> - 2010-03-04 18:56:56
|
Revision: 22761
http://gmod.svn.sourceforge.net/gmod/?rev=22761&view=rev
Author: gk_fan
Date: 2010-03-04 18:56:35 +0000 (Thu, 04 Mar 2010)
Log Message:
-----------
Updated version info for new release.
Modified Paths:
--------------
apollo/trunk/src/java/apollo/main/Version.java
Modified: apollo/trunk/src/java/apollo/main/Version.java
===================================================================
--- apollo/trunk/src/java/apollo/main/Version.java 2010-03-04 18:54:32 UTC (rev 22760)
+++ apollo/trunk/src/java/apollo/main/Version.java 2010-03-04 18:56:35 UTC (rev 22761)
@@ -7,7 +7,7 @@
*/
public class Version {
- public static String version = "Apollo Genome Annotation and Curation Tool, version 1.11.1";
+ public static String version = "Apollo Genome Annotation and Curation Tool, version 1.11.2";
public static String getVersion() {
String timestamp = Config.getTimestamp();
if (timestamp == null)
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|
From: <gk...@us...> - 2010-03-04 18:52:14
|
Revision: 22759
http://gmod.svn.sourceforge.net/gmod/?rev=22759&view=rev
Author: gk_fan
Date: 2010-03-04 18:52:04 +0000 (Thu, 04 Mar 2010)
Log Message:
-----------
Fixed issue with one-level annotations not being generated correctly by wrapping them in an AnnotatedFeatureI object.
Modified Paths:
--------------
apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-03-04 16:54:07 UTC (rev 22758)
+++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java 2010-03-04 18:52:04 UTC (rev 22759)
@@ -690,6 +690,14 @@
}
if (!added) {
if (gff.isAnnotation()) {
+ // need to wrap one-level annotations (non-genes) in a AnnotationFeatureI otherwise Apollo isn't happy
+ if (feat.isAnnotTop() && !gff.getType().contains("gene")) {
+ AnnotatedFeatureI fs = new AnnotatedFeature();
+ fs.addFeature(feat);
+ fs.setStrand(feat.getStrand());
+ fs.setId(feat.getId() + "-fs");
+ feat = fs;
+ }
// arbitrarily add strand-less features to plus strand
if (feat.getStrand() == 0) {
annots.getForwardSet().addFeature(feat);
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|
|
From: <gk...@us...> - 2010-02-01 21:24:54
|
Revision: 22647
http://gmod.svn.sourceforge.net/gmod/?rev=22647&view=rev
Author: gk_fan
Date: 2010-02-01 21:24:41 +0000 (Mon, 01 Feb 2010)
Log Message:
-----------
Fixed issue where when analysis table is cached, if no configured one level result type is found in the analysis, it would fetch all results in the given range (since the where clause was not set for explicit filtering)
Modified Paths:
--------------
apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java
Modified: apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java 2010-02-01 20:58:50 UTC (rev 22646)
+++ apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java 2010-02-01 21:24:41 UTC (rev 22647)
@@ -2937,8 +2937,13 @@
where.add("af.analysis_id", "a.analysis_id");
}
- try {
- where.add(getChadoProgramWhereClause(programs, "af", analysisAlias));
+ try {
+ String chadoProgramWhereClause = getChadoProgramWhereClause(programs, "af", analysisAlias);
+ // no analysis found for configured programs
+ if (chadoProgramWhereClause.length() == 0) {
+ return;
+ }
+ where.add(chadoProgramWhereClause);
}
catch (AnalysisException e) {
logger.error("unable to retrieve one-level results: " + e.getMessage());
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|
|
From: <gk...@us...> - 2010-01-08 17:12:22
|
Revision: 22510
http://gmod.svn.sourceforge.net/gmod/?rev=22510&view=rev
Author: gk_fan
Date: 2010-01-08 17:12:13 +0000 (Fri, 08 Jan 2010)
Log Message:
-----------
Changed XML parsing of BLAST results to use URIs instead of InputStreams, as it was causing errors in Java Web Start mode.
Modified Paths:
--------------
apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java
apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java
apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java
Modified: apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java
===================================================================
--- apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java 2010-01-08 16:53:07 UTC (rev 22509)
+++ apollo/trunk/src/java/apollo/analysis/BlastXMLParser.java 2010-01-08 17:12:13 UTC (rev 22510)
@@ -1,8 +1,6 @@
package apollo.analysis;
import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
@@ -12,8 +10,6 @@
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
-import org.xml.sax.EntityResolver;
-import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import apollo.datamodel.FeaturePair;
@@ -44,23 +40,17 @@
{
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
db = dbf.newDocumentBuilder();
- db.setEntityResolver(new EntityResolver() {
- public InputSource resolveEntity(String publicId, String systemId)
- {
- return new InputSource(new StringReader(""));
- }
- });
}
- public String parse(InputStream is, StrandedFeatureSetI results) throws SAXException, IOException, BlastXMLParserException
+ public String parse(String uri, StrandedFeatureSetI results) throws SAXException, IOException, BlastXMLParserException
{
- return parse(is, results, 1, 0, 0);
+ return parse(uri, results, 1, 0, 0);
}
- public String parse(InputStream is, StrandedFeatureSetI results, int strand, int genomicLength, int offset) throws
+ public String parse(String uri, StrandedFeatureSetI results, int strand, int genomicLength, int offset) throws
SAXException, IOException, BlastXMLParserException
{
- Document doc = db.parse(is);
+ Document doc = db.parse(uri);
String blast = getTextContent(doc.getElementsByTagName("BlastOutput_program").item(0));
String db = getTextContent(doc.getElementsByTagName("BlastOutput_db").item(0));
String type = blast + ":" + db;
Modified: apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java
===================================================================
--- apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java 2010-01-08 16:53:07 UTC (rev 22509)
+++ apollo/trunk/src/java/apollo/analysis/BlastXMLParserTest.java 2010-01-08 17:12:13 UTC (rev 22510)
@@ -1,13 +1,7 @@
package apollo.analysis;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
+import java.io.File;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
import apollo.datamodel.StrandedFeatureSet;
import junit.framework.TestCase;
@@ -16,10 +10,10 @@
public void testParse() throws Exception
{
- FileInputStream fis = new FileInputStream("/Users/elee/blah/blast_3.xml");
+ File f = new File("/Users/elee/blah/blast_3.xml");
BlastXMLParser parser = new BlastXMLParser();
StrandedFeatureSet results = new StrandedFeatureSet();
- parser.parse(fis, results);
+ parser.parse(f.toURL().toString(), results);
}
}
Modified: apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java
===================================================================
--- apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java 2010-01-08 16:53:07 UTC (rev 22509)
+++ apollo/trunk/src/java/apollo/analysis/RemoteBlastNCBI.java 2010-01-08 17:12:13 UTC (rev 22510)
@@ -30,6 +30,7 @@
private static final String ENCODING = "UTF-8";
private static final String BLAST_URL = "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?";
+ //private static final String BLAST_URL = "http://130.14.29.110/blast/Blast.cgi?";
private static final int SLEEP = 3000;
private static final Pattern RID_PATTERN = Pattern.compile("^\\s*RID\\s*=\\s*(\\w+)$");
private static final Pattern RTOE_PATTERN = Pattern.compile("^\\s*RTOE\\s*=\\s*(\\d+)$");
@@ -285,13 +286,14 @@
}
is.close();
getUrl = new URL(createGetUrl(req, false));
- is = getUrl.openStream();
+
+ //is = getUrl.openStream();
BlastXMLParser parser = new BlastXMLParser();
- String type = parser.parse(is, cs.getResults(), strand, genomicLength, offset);
+ String type = parser.parse(getUrl.toString(), cs.getResults(), strand, genomicLength, offset);
- is.close();
+ //is.close();
if (cs.getResults().getForwardSet() != null) {
System.out.println("forward hits: " + cs.getResults().getForwardSet().size());
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|
|
From: <gk...@us...> - 2010-01-08 00:09:00
|
Revision: 22508
http://gmod.svn.sourceforge.net/gmod/?rev=22508&view=rev
Author: gk_fan
Date: 2010-01-08 00:08:52 +0000 (Fri, 08 Jan 2010)
Log Message:
-----------
Chado panel gets initialized correctly now, even in Web Start mode.
Modified Paths:
--------------
apollo/trunk/src/java/apollo/dataadapter/chado/ChadoAdapterGUI.java
Modified: apollo/trunk/src/java/apollo/dataadapter/chado/ChadoAdapterGUI.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/chado/ChadoAdapterGUI.java 2010-01-07 23:54:39 UTC (rev 22507)
+++ apollo/trunk/src/java/apollo/dataadapter/chado/ChadoAdapterGUI.java 2010-01-08 00:08:52 UTC (rev 22508)
@@ -689,10 +689,12 @@
seqChoiceComboBox.addItemListener(this);
seqChoiceButton.addActionListener(this);
+ /*
// OP_READ_DATA
if (getOperation().equals(ApolloDataAdapterI.OP_READ_DATA)) {
+ */
makeReadDataUI();
- }
+ //}
// Nothing else supported yet
// else {
// logger.error(this.getClass() + ": makeUI() called with unsupported operation " + this.operation);
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|
|
From: <gk...@us...> - 2009-12-21 19:24:15
|
Revision: 22445
http://gmod.svn.sourceforge.net/gmod/?rev=22445&view=rev
Author: gk_fan
Date: 2009-12-21 19:23:57 +0000 (Mon, 21 Dec 2009)
Log Message:
-----------
+ If running in Web Start, will now extract "restriction_enzymes.dat" from
the jar file
Modified Paths:
--------------
apollo/trunk/src/java/apollo/gui/tweeker/RestrictionEnzymeSelector.java
Modified: apollo/trunk/src/java/apollo/gui/tweeker/RestrictionEnzymeSelector.java
===================================================================
--- apollo/trunk/src/java/apollo/gui/tweeker/RestrictionEnzymeSelector.java 2009-12-21 18:35:28 UTC (rev 22444)
+++ apollo/trunk/src/java/apollo/gui/tweeker/RestrictionEnzymeSelector.java 2009-12-21 19:23:57 UTC (rev 22445)
@@ -31,6 +31,7 @@
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
+import apollo.config.Config;
import apollo.datamodel.SequenceI;
import apollo.datamodel.Range;
import apollo.datamodel.RangeI;
@@ -181,8 +182,22 @@
/** Parse restriction enzyme file into vector */
private Vector getRestrictionEnzymes() {
- String root = System.getProperty("APOLLO_ROOT");
- File resEnzFile = new File(root+"/data/restriction_enzymes.dat");
+ //String root = System.getProperty("APOLLO_ROOT");
+ //File resEnzFile = new File(root+"/data/restriction_enzymes.dat");
+ String resEnzFileName = "restriction_enzymes.dat";
+ String resEnzFileDir = "data";
+ String resEnzPath = apollo.util.IOUtil.findFile(resEnzFileDir + "/" + resEnzFileName);
+ File resEnzFile = new File(Config.getRootDir() + "/" + resEnzFileDir + "/" + resEnzFileName);
+ if (resEnzPath == null || Config.isJavaWebStartApplication()) {
+ try {
+ Config.ensureExists(resEnzFile, resEnzFileName);
+ }
+ catch (Exception e) {
+ logger.warn("Couldn't find or create " + resEnzFileName);
+ return restrictionEnzymes;
+ }
+ }
+
try {
// would be nice to file in relative way
// this might just work for jar files? thought it would work for
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|
|
From: <gk...@us...> - 2009-11-05 16:09:59
|
Revision: 22235
http://gmod.svn.sourceforge.net/gmod/?rev=22235&view=rev
Author: gk_fan
Date: 2009-11-05 16:09:47 +0000 (Thu, 05 Nov 2009)
Log Message:
-----------
+ Fixed support for Chado instances where "searchHitsHaveFeatLocs"
are set to false (apparently FlyBase still uses Chado this way...)
Modified Paths:
--------------
apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java
Modified: apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java 2009-11-05 08:55:38 UTC (rev 22234)
+++ apollo/trunk/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java 2009-11-05 16:09:47 UTC (rev 22235)
@@ -2055,8 +2055,8 @@
"leafFeat.type_id as featureTypeId, "+
lazySelect +
"tgtFeatLoc.residue_info AS target_residue_info "+
- (joinWithFeatureProp ? ", fp." + pvalCol + " AS feature_prop " : "") + ", " +
- "leafToParent.object_id AS parent_id" +
+ (joinWithFeatureProp ? ", fp." + pvalCol + " AS feature_prop " : "") +
+ (getChadoInstance().searchHitsHaveFeatLocs() ? ", leafToParent.object_id AS parent_id" : "") +
"\nFROM featureloc leafFeatLoc, feature leafFeat, " +
(joinWithFeatureProp ? "featureprop fp, " : "") +
@@ -2086,7 +2086,7 @@
// o2." + abbrevCol
+ ", tgtFeat.uniquename "
+ ", leafFeatLoc.strand "
- + ", leafToParent.object_id";
+ + (getChadoInstance().searchHitsHaveFeatLocs() ? ", leafToParent.object_id" : "");
ResultSet rs = executeLoggedSelectQuery("addSearchHits", c, sql);
@@ -2128,7 +2128,7 @@
String targetResidues = null;
if (setTargetSeqs && !getTargetSeqsSeparately)
targetResidues = rs.getString("target_residues");
- long parentId = rs.getLong("parent_id");
+ long parentId = getChadoInstance().searchHitsHaveFeatLocs() ? rs.getLong("parent_id") : 0;
String featName = null;
String tgtFeatName = null;
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|
|
From: elee <gk...@us...> - 2009-08-10 14:35:55
|
Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gff3 In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv25339 Modified Files: GFF3Adapter.java Log Message: + Check to make sure a match has the hit sequence data in case of id collisions before comparison Index: GFF3Adapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gff3/GFF3Adapter.java,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -d -r1.18 -r1.19 *** GFF3Adapter.java 15 Jul 2009 20:34:44 -0000 1.18 --- GFF3Adapter.java 10 Aug 2009 14:35:44 -0000 1.19 *************** *** 355,359 **** // collisions back - if there's a collision, append a counter to the sequence // identifier ! if (seqs.containsKey(hitSeq.getName()) && !seqs.get(hitSeq.getName()).getResidues().equals(hitSeq.getResidues())) { String oldHitName = hitSeq.getName(); seqIds.put(hitSeq.getName(), seqIds.get(hitSeq.getName()) + 1); --- 355,360 ---- // collisions back - if there's a collision, append a counter to the sequence // identifier ! ! if (seqs.containsKey(hitSeq.getName()) && hitSeq.getResidues() != null && !seqs.get(hitSeq.getName()).getResidues().equals(hitSeq.getResidues())) { String oldHitName = hitSeq.getName(); seqIds.put(hitSeq.getName(), seqIds.get(hitSeq.getName()) + 1); |
|
From: elee <gk...@us...> - 2009-07-24 19:57:00
|
Update of /cvsroot/gmod/apollo/src/java/apollo/analysis In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv28330 Modified Files: AnalysisGUI.java BlastXMLParser.java Log Message: + Fixed some offset issues when dealing with analysis on minus strand Index: AnalysisGUI.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/analysis/AnalysisGUI.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** AnalysisGUI.java 17 Jul 2009 18:28:46 -0000 1.3 --- AnalysisGUI.java 24 Jul 2009 19:56:48 -0000 1.4 *************** *** 603,614 **** int seqStart; int seqEnd; ! if (strand == 1) { ! seqStart = start - cs.getLow(); ! seqEnd = end - cs.getLow() + 1; ! } ! else { ! seqStart = start - cs.getLow() - 1; ! seqEnd = end - cs.getLow(); ! } SequenceI region = new Sequence(cs.getRefSequence().getName(), cs.getRefSequence().getResidues().substring(seqStart, seqEnd)); //String type = blast.runAnalysis(cs, cs.getRefSequence().getSubSequence(start, end), strand, start - 1); --- 603,608 ---- int seqStart; int seqEnd; ! seqStart = start - cs.getLow(); ! seqEnd = end - cs.getLow() + 1; SequenceI region = new Sequence(cs.getRefSequence().getName(), cs.getRefSequence().getResidues().substring(seqStart, seqEnd)); //String type = blast.runAnalysis(cs, cs.getRefSequence().getSubSequence(start, end), strand, start - 1); Index: BlastXMLParser.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/analysis/BlastXMLParser.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** BlastXMLParser.java 27 Feb 2009 17:03:09 -0000 1.2 --- BlastXMLParser.java 24 Jul 2009 19:56:48 -0000 1.3 *************** *** 150,155 **** } else { ! queryBegin = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-to").item(0))); ! queryEnd = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-from").item(0))); queryStrand *= -1; } --- 150,155 ---- } else { ! queryBegin = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-to").item(0))) + 1; ! queryEnd = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-from").item(0))) + 1; queryStrand *= -1; } |
|
From: elee <gk...@us...> - 2009-07-17 18:28:59
|
Update of /cvsroot/gmod/apollo/src/java/apollo/analysis In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv4931 Modified Files: AnalysisGUI.java Log Message: + Due to issues with different Sequence.getSubsequence() implementations, ended up writing outside one to behave the same regardless of Sequence Index: AnalysisGUI.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/analysis/AnalysisGUI.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** AnalysisGUI.java 27 Feb 2009 17:03:09 -0000 1.2 --- AnalysisGUI.java 17 Jul 2009 18:28:46 -0000 1.3 *************** *** 32,35 **** --- 32,37 ---- import apollo.config.TierProperty; import apollo.datamodel.CurationSet; + import apollo.datamodel.Sequence; + import apollo.datamodel.SequenceI; import apollo.gui.genomemap.StrandedZoomableApolloPanel; import apollo.gui.synteny.CurationManager; *************** *** 598,602 **** getOptions()); CurationSet cs = CurationManager.getActiveCurationState().getCurationSet(); ! String type = blast.runAnalysis(cs, cs.getRefSequence().getSubSequence(start, end), strand, start - 1); AnalysisFilter filter = new AnalysisFilter(); AnalysisInput ai = new AnalysisInput(); --- 600,617 ---- getOptions()); CurationSet cs = CurationManager.getActiveCurationState().getCurationSet(); ! // too much weirdness going on with the different implementation of Sequence objects, just create our own subsequence here ! int seqStart; ! int seqEnd; ! if (strand == 1) { ! seqStart = start - cs.getLow(); ! seqEnd = end - cs.getLow() + 1; ! } ! else { ! seqStart = start - cs.getLow() - 1; ! seqEnd = end - cs.getLow(); ! } ! SequenceI region = new Sequence(cs.getRefSequence().getName(), cs.getRefSequence().getResidues().substring(seqStart, seqEnd)); ! //String type = blast.runAnalysis(cs, cs.getRefSequence().getSubSequence(start, end), strand, start - 1); ! String type = blast.runAnalysis(cs, region, strand, start - 1); AnalysisFilter filter = new AnalysisFilter(); AnalysisInput ai = new AnalysisInput(); |
|
From: elee <gk...@us...> - 2009-07-17 02:30:29
|
Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv17977/dataadapter/chado/jdbc Modified Files: FlybaseChadoInstance.java Log Message: + CurationSet for genomic region is now set to be of strand 1 (needed for SequenceAligner) Index: FlybaseChadoInstance.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/FlybaseChadoInstance.java,v retrieving revision 1.68 retrieving revision 1.69 diff -C2 -d -r1.68 -r1.69 *** FlybaseChadoInstance.java 5 Jan 2009 23:48:54 -0000 1.68 --- FlybaseChadoInstance.java 17 Jul 2009 02:30:20 -0000 1.69 *************** *** 301,304 **** --- 301,305 ---- cset = new CurationSet(); + cset.setStrand(1); //cset.setAssemblyType(seqType); String srcFeatureType = featLocImp.getSrcFeatureType(); |
|
From: elee <gk...@us...> - 2009-07-15 20:34:54
|
Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gff3 In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv616/dataadapter/gff3 Modified Files: GFF3Adapter.java GFF3Entry.java Log Message: + Lots of GFF3 bug fixes (thanks Carson Holt!) Index: GFF3Adapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gff3/GFF3Adapter.java,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 *** GFF3Adapter.java 7 Jul 2009 00:41:35 -0000 1.17 --- GFF3Adapter.java 15 Jul 2009 20:34:44 -0000 1.18 *************** *** 147,151 **** return curation; } ! /** Add GFF3 data to currently existing CurationSet * --- 147,151 ---- return curation; } ! /** Add GFF3 data to currently existing CurationSet * *************** *** 161,165 **** return true; } ! /** Commit data --- 161,165 ---- return true; } ! /** Commit data *************** *** 233,237 **** apolloData.getCompositeDataHolder().getCurationSet(0); } ! /** Write seqs as FASTA format * --- 233,237 ---- apolloData.getCompositeDataHolder().getCurationSet(0); } ! /** Write seqs as FASTA format * *************** *** 288,292 **** entry.setType("mRNA"); int tStart = trans.getTranslationStart(); ! int tEnd = trans.getTranslationEnd(); if (trans.getStrand() == -1) { int tmp = tStart; --- 288,292 ---- entry.setType("mRNA"); int tStart = trans.getTranslationStart(); ! int tEnd = trans.getLastBaseOfStopCodon(); //trans.getTranslationEnd(); if (trans.getStrand() == -1) { int tmp = tStart; *************** *** 448,589 **** //annotations StrandedFeatureSetI annots = curation.getAnnots() == null ? ! new StrandedFeatureSet(new AnnotatedFeature(), ! new AnnotatedFeature()) : ! curation.getAnnots(); ! //evidences ! StrandedFeatureSetI results = curation.getResults() == null ? ! new StrandedFeatureSet(new FeatureSet(), new FeatureSet()) : ! curation.getResults(); ! br.mark(1); ! int c; ! Map<String, GFF3Data> gffMap = new TreeMap<String, GFF3Data>(); ! Map<String, int[]> cdsCoords = new TreeMap<String, int[]>(); ! while ((c = br.read()) != -1) { ! //embedded FASTA ! if (c == '>') { ! br.reset(); ! //no FASTA parsed from separate file, process embedded ! if (isFastaFromGff() || seqs.isEmpty()) { ! parseSeq(br); ! } ! break; ! } ! else { ! line = (char)c + br.readLine(); ! if (line.charAt(0) == '#') { ! if (line.charAt(1) == '#') { ! //parse pragmas ! String []tokens = line.split("\\s+"); ! //get the reference sequence coordinates ! if (tokens[0].equals("##sequence-region")) { ! refId = tokens[1]; ! if (!setRefSeq && !refId.equals(curation.getRefSequence().getName())) { ! throw new ApolloAdapterException("Trying to append data for sequence " + ! refId + " when current data loaded is for " + ! curation.getRefSequence().getName()); } ! curation.setStrand(1); ! curation.setLow(Integer.parseInt(tokens[2])); ! curation.setHigh(Integer.parseInt(tokens[3])); ! } ! } ! } ! //parse entries ! else { ! //skip blank lines ! if (line.length() == 0) { ! continue; ! } ! GFF3Entry entry = new GFF3Entry(line); ! //if genomic sequence already loaded, make sure that entry's genomic identifiers match ! if (!setRefSeq && !entry.getReferenceId().matches(curation.getRefSequence().getName())) { ! if (!invalidSeqIds.contains(entry.getReferenceId())) { ! apollo.util.IOUtil.errorDialog("Skipping entry for sequence " + ! entry.getReferenceId() + " when current data loaded is for " + ! curation.getRefSequence().getName()); ! invalidSeqIds.add(entry.getReferenceId()); ! } ! continue; ! } ! //if there was no ##sequence pragma, use the refseq id in the first entry ! if (refId == null) { ! refId = entry.getReferenceId(); ! } ! Pair<IdentifiedObject, String> term = oboParser.getTermByName(entry.getType()); ! if (term == null) { ! //throw new ApolloAdapterException("Invalid GFF3 file: " + entry.getType() + " is not a valid SO term"); ! if (!invalidSOTerms.contains(entry.getType())) { ! apollo.util.IOUtil.errorDialog("Invalid GFF3 file: " + entry.getType() + " is not a valid SO term"); ! invalidSOTerms.add(entry.getType()); ! } ! continue; ! } ! if (!entry.getType().equals(term.getSecond())) { ! logger.info("GFF3 type " + entry.getType() + " does not match case for SO term " + term.getSecond() + ! "(" + term.getFirst().getID() + ")"); ! } ! if (entry.getType().equals("CDS")) { ! processCds(entry, cdsCoords); ! } ! else if (entry.getType().equals("five_prime_UTR") || ! entry.getType().equals("three_prime_UTR")) { ! } ! else if (entry.getType().equals("protein")) { ! } ! else { ! if (!gffMap.containsKey(entry.getId())) { ! try { ! gffMap.put(entry.getId(), new GFF3Data(entry, entry.createFeature(oboParser))); } ! catch (ClassNotFoundException e) { ! throw new ApolloAdapterException("Cannot locate Apollo datamodel class: " + e.getMessage()); } ! catch (IllegalAccessException e) { ! throw new ApolloAdapterException(e); } ! catch (InstantiationException e) { ! throw new ApolloAdapterException("Cannot instantiate class: " + e.getMessage()); } } - else { - logger.warn("Multiple features with id " + entry.getId() + - ". Only processing the first one."); - } - } - } - } - br.mark(1); - } ! if (setRefSeq) { ! SequenceI refSeq = refId != null ? seqs.get(refId) : null; ! if (refSeq == null) { ! //if no exact id match was found and there is ONLY ONE sequence provided ! //then assume that sequence is the genomic sequence... ! if (seqs.size() == 1) { ! Map.Entry<String, SequenceI> entry = seqs.entrySet().iterator().next(); ! refSeq = entry.getValue(); ! logger.warn("No sequence data found for " + refId + ". Using sequence " + ! entry.getKey() + " instead."); ! } ! else { ! throw new ApolloAdapterException("No sequence data found for " + ! refId); ! } ! } ! curation.setRefSequence(refSeq); ! //if there was no ##sequence pragma, set the curation bounds as the refseq length ! if (curation.getLow() == -1) { ! curation.setLow(1); ! } ! if (curation.getHigh() == -1) { ! curation.setHigh(refSeq.getLength()); ! } ! } ! ! processFeatures(annots, results, gffMap, cdsCoords, curation); ! curation.setAnnots(annots); ! curation.setResults(results); } catch (IOException e) { --- 448,589 ---- //annotations StrandedFeatureSetI annots = curation.getAnnots() == null ? ! new StrandedFeatureSet(new AnnotatedFeature(), ! new AnnotatedFeature()) : ! curation.getAnnots(); ! //evidences ! StrandedFeatureSetI results = curation.getResults() == null ? ! new StrandedFeatureSet(new FeatureSet(), new FeatureSet()) : ! curation.getResults(); ! br.mark(1); ! int c; ! Map<String, GFF3Data> gffMap = new TreeMap<String, GFF3Data>(); ! Map<String, int[]> cdsCoords = new TreeMap<String, int[]>(); ! while ((c = br.read()) != -1) { ! //embedded FASTA ! if (c == '>') { ! br.reset(); ! //no FASTA parsed from separate file, process embedded ! if (isFastaFromGff() || seqs.isEmpty()) { ! parseSeq(br); ! } ! break; } ! else { ! line = (char)c + br.readLine(); ! if (line.charAt(0) == '#') { ! if (line.charAt(1) == '#') { ! //parse pragmas ! String []tokens = line.split("\\s+"); ! //get the reference sequence coordinates ! if (tokens[0].equals("##sequence-region")) { ! refId = tokens[1]; ! if (!setRefSeq && !refId.equals(curation.getRefSequence().getName())) { ! throw new ApolloAdapterException("Trying to append data for sequence " + ! refId + " when current data loaded is for " + ! curation.getRefSequence().getName()); ! } ! curation.setStrand(1); ! curation.setLow(Integer.parseInt(tokens[2])); ! curation.setHigh(Integer.parseInt(tokens[3])); ! } ! } ! } ! //parse entries ! else { ! //skip blank lines ! if (line.length() == 0) { ! continue; ! } ! GFF3Entry entry = new GFF3Entry(line); ! //if genomic sequence already loaded, make sure that entry's genomic identifiers match ! if (!setRefSeq && !entry.getReferenceId().matches(curation.getRefSequence().getName())) { ! if (!invalidSeqIds.contains(entry.getReferenceId())) { ! apollo.util.IOUtil.errorDialog("Skipping entry for sequence " + ! entry.getReferenceId() + " when current data loaded is for " + ! curation.getRefSequence().getName()); ! invalidSeqIds.add(entry.getReferenceId()); ! } ! continue; ! } ! //if there was no ##sequence pragma, use the refseq id in the first entry ! if (refId == null) { ! refId = entry.getReferenceId(); ! } ! Pair<IdentifiedObject, String> term = oboParser.getTermByName(entry.getType()); ! if (term == null) { ! //throw new ApolloAdapterException("Invalid GFF3 file: " + entry.getType() + " is not a valid SO term"); ! if (!invalidSOTerms.contains(entry.getType())) { ! apollo.util.IOUtil.errorDialog("Invalid GFF3 file: " + entry.getType() + " is not a valid SO term"); ! invalidSOTerms.add(entry.getType()); ! } ! continue; ! } ! if (!entry.getType().equals(term.getSecond())) { ! logger.info("GFF3 type " + entry.getType() + " does not match case for SO term " + term.getSecond() + ! "(" + term.getFirst().getID() + ")"); ! } ! if (entry.getType().equals("CDS")) { ! processCds(entry, cdsCoords); ! } ! else if (entry.getType().equals("five_prime_UTR") || ! entry.getType().equals("three_prime_UTR")) { ! } ! else if (entry.getType().equals("protein")) { ! } ! else { ! if (!gffMap.containsKey(entry.getId())) { ! try { ! gffMap.put(entry.getId(), new GFF3Data(entry, entry.createFeature(oboParser))); ! } ! catch (ClassNotFoundException e) { ! throw new ApolloAdapterException("Cannot locate Apollo datamodel class: " + e.getMessage()); ! } ! catch (IllegalAccessException e) { ! throw new ApolloAdapterException(e); ! } ! catch (InstantiationException e) { ! throw new ApolloAdapterException("Cannot instantiate class: " + e.getMessage()); ! } ! } ! else { ! logger.warn("Multiple features with id " + entry.getId() + ! ". Only processing the first one."); ! } ! } ! } } ! br.mark(1); ! } ! ! if (setRefSeq) { ! SequenceI refSeq = refId != null ? seqs.get(refId) : null; ! if (refSeq == null) { ! //if no exact id match was found and there is ONLY ONE sequence provided ! //then assume that sequence is the genomic sequence... ! if (seqs.size() == 1) { ! Map.Entry<String, SequenceI> entry = seqs.entrySet().iterator().next(); ! refSeq = entry.getValue(); ! logger.warn("No sequence data found for " + refId + ". Using sequence " + ! entry.getKey() + " instead."); ! } ! else { ! throw new ApolloAdapterException("No sequence data found for " + ! refId); ! } } ! curation.setRefSequence(refSeq); ! //if there was no ##sequence pragma, set the curation bounds as the refseq length ! if (curation.getLow() == -1) { ! curation.setLow(1); } ! if (curation.getHigh() == -1) { ! curation.setHigh(refSeq.getLength()); } } ! processFeatures(annots, results, gffMap, cdsCoords, curation); ! curation.setAnnots(annots); ! curation.setResults(results); } catch (IOException e) { *************** *** 599,748 **** Map<String, FeatureSetI[]> resultSets = new TreeMap<String, FeatureSetI[]>(); ! Set<String> errors = new HashSet<String>(); ! Set<GFF3Data> matches = new HashSet<GFF3Data>(); ! for (Map.Entry<String, GFF3Data> mapEntry : gffMap.entrySet()) { ! GFF3Data data = mapEntry.getValue(); ! GFF3Entry gff = data.getEntry(); ! SeqFeatureI feat = data.getFeat(); ! feat.setRefSequence(curation.getRefSequence()); ! if (!gff.isAnnotation()) { ! processEvidence(feat); ! } ! // add matches for post processing if they're missing match_part features ! if (gff.getType().equals("match")) { ! matches.add(data); ! } ! boolean added = false; ! List<String> pids = gff.getAttributeValues("Parent"); ! if (pids != null) { ! int pnum = 0; ! for (String pid : pids) { ! GFF3Data pdata = gffMap.get(pid); ! if (gff.isAnnotation()) { ! SeqFeatureI parent = pdata.getFeat(); ! if (!feat.isTranscript() && !feat.isExon()) { ! if (!errors.contains(feat.getName())) { ! IOUtil.errorDialog("Only transcripts and exons can be children of annotations: " + ! feat.getName() + "[" + feat.getFeatureType() + "]"); ! errors.add(feat.getName()); } ! added = true; continue; } ! if (feat.isExon() && !parent.isTranscript()) { ! if (!errors.contains(feat.getName())) { ! IOUtil.errorDialog("Exons can only be children of transcripts: " + feat.getName() + " -> " + ! parent.getName() + "[" + parent.getFeatureType() + "]"); ! errors.add(feat.getName()); } added = true; ! continue; } } ! ++pnum; ! if (pdata == null) { //orphan ! logger.warn("Missing parent " + pid + " for " + ! gff.getName()); ! continue; ! } ! if (pnum > 1) { ! if (pnum == 2) { ! feat.setId(feat.getId() + "-1"); } - feat = feat.cloneFeature(); - feat.setId(feat.getId().replaceFirst("-\\d+$", - "-" + pnum)); } if (gff.isAnnotation()) { ! processAnnotation(data, pdata.getFeat(), cdsCoords); ! } ! try { ! pdata.getFeat().addFeature(feat); ! added = true; } ! catch (ClassCastException e) { /* ! throw new ApolloAdapterException("Cannot add " + feat + ! "(" + data.getEntry().getType() + ")" + " to " + ! pdata.getFeat() + "(" + pdata.getEntry().getType() + ! ")"); */ - logger.warn("Cannot add " + feat + - "(" + data.getEntry().getType() + ")" + " to " + - pdata.getFeat() + "(" + pdata.getEntry().getType() + - ")"); } } } ! //a transcript can potentially not have a gene associated with it, in which ! //case we need to generate one (the GFF3 spec doesn't REQUIRE a transcript ! //to have a gene, which seems kind of silly to me...) ! else { ! if (!feat.isAnnotTop()) { ! if (gff.isAnnotation()) { ! logger.warn("No parent feature found for " + feat + ! "(" + gff.getType() + "). Generating dummy parent feature."); ! generateParent(feat, annots); ! added = true; } ! } ! } ! if (!added) { ! if (gff.isAnnotation()) { ! annots.addFeature(feat); ! } ! else { ! processEvidence(feat); ! FeatureSetI []fsArray = resultSets.get(gff.getSource()); ! if (fsArray == null) { ! fsArray = new FeatureSet[2]; ! resultSets.put(gff.getSource(), fsArray); } ! int arrayIdx = gff.getStrand() == 1 ? 1 : 0; ! FeatureSetI fs = fsArray[arrayIdx]; ! if (fs == null) { ! fs = new FeatureSet(gff.getSource(), gff.getStrand()); ! fsArray[arrayIdx] = fs; } - fs.addFeature(feat); - /* - results.addFeature(feat); - */ } } ! } ! ! // add FeaturePair objects to any matches with no match_part children ! for (GFF3Data data : matches) { ! SeqFeatureI match = data.getFeat(); ! if (match.getFeatures().size() == 0) { ! GFF3Entry matchPart = new GFF3Entry(data.getEntry().toString()); ! matchPart.setType("match_part"); ! try { ! SeqFeatureI matchPartFeat = matchPart.createFeature(oboParser); ! processEvidence(matchPartFeat); ! match.addFeature(matchPartFeat); ! } ! catch (ClassNotFoundException e) { ! throw new ApolloAdapterException("Cannot locate Apollo datamodel class: " + e.getMessage()); ! } ! catch (IllegalAccessException e) { ! throw new ApolloAdapterException(e); } ! catch (InstantiationException e) { ! throw new ApolloAdapterException("Cannot instantiate class: " + e.getMessage()); } } ! } ! ! for (Map.Entry<String, FeatureSetI[]> e : resultSets.entrySet()) { ! if (e.getValue()[0] != null) { ! results.addFeature(e.getValue()[0]); ! } ! if (e.getValue()[1] != null) { ! results.addFeature(e.getValue()[1]); ! } ! } ! setTranslationEnds(gffMap, cdsCoords); } --- 599,754 ---- Map<String, FeatureSetI[]> resultSets = new TreeMap<String, FeatureSetI[]>(); ! Set<String> errors = new HashSet<String>(); ! Set<GFF3Data> matches = new HashSet<GFF3Data>(); ! for (Map.Entry<String, GFF3Data> mapEntry : gffMap.entrySet()) { ! GFF3Data data = mapEntry.getValue(); ! GFF3Entry gff = data.getEntry(); ! SeqFeatureI feat = data.getFeat(); ! feat.setRefSequence(curation.getRefSequence()); ! if (!gff.isAnnotation()) { ! processEvidence(feat); ! } ! // add matches for post processing if they're missing match_part features ! if (gff.getType().equals("match")) { ! matches.add(data); ! } ! boolean added = false; ! List<String> pids = gff.getAttributeValues("Parent"); ! if (pids != null) { ! int pnum = 0; ! for (String pid : pids) { ! GFF3Data pdata = gffMap.get(pid); ! if (gff.isAnnotation()) { ! SeqFeatureI parent = pdata.getFeat(); ! if (!feat.isTranscript() && !feat.isExon()) { ! if (!errors.contains(feat.getName())) { ! IOUtil.errorDialog("Only transcripts and exons can be children of annotations: " + ! feat.getName() + "[" + feat.getFeatureType() + "]"); ! errors.add(feat.getName()); ! } ! added = true; ! continue; } ! if (feat.isExon() && !parent.isTranscript()) { ! if (!errors.contains(feat.getName())) { ! IOUtil.errorDialog("Exons can only be children of transcripts: " + feat.getName() + " -> " + ! parent.getName() + "[" + parent.getFeatureType() + "]"); ! errors.add(feat.getName()); ! } ! added = true; ! continue; ! } ! } ! ++pnum; ! if (pdata == null) { //orphan ! logger.warn("Missing parent " + pid + " for " + ! gff.getName()); continue; } ! if (pnum > 1) { ! if (pnum == 2) { ! feat.setId(feat.getId() + "-1"); } + feat = feat.cloneFeature(); + feat.setId(feat.getId().replaceFirst("-\\d+$", + "-" + pnum)); + } + if (gff.isAnnotation()) { + processAnnotation(data, pdata.getFeat(), cdsCoords); + } + try { + pdata.getFeat().addFeature(feat); added = true; ! } ! catch (ClassCastException e) { ! /* ! throw new ApolloAdapterException("Cannot add " + feat + ! "(" + data.getEntry().getType() + ")" + " to " + ! pdata.getFeat() + "(" + pdata.getEntry().getType() + ! ")"); ! */ ! logger.warn("Cannot add " + feat + ! "(" + data.getEntry().getType() + ")" + " to " + ! pdata.getFeat() + "(" + pdata.getEntry().getType() + ! ")"); } } ! } ! //a transcript can potentially not have a gene associated with it, in which ! //case we need to generate one (the GFF3 spec doesn't REQUIRE a transcript ! //to have a gene, which seems kind of silly to me...) ! else { ! if (!feat.isAnnotTop()) { ! if (gff.isAnnotation()) { ! logger.warn("No parent feature found for " + feat + ! "(" + gff.getType() + "). Generating dummy parent feature."); ! generateParent(feat, annots); ! added = true; } } + } + if (!added) { if (gff.isAnnotation()) { ! // arbitrarily add strand-less features to plus strand ! if (feat.getStrand() == 0) { ! annots.getForwardSet().addFeature(feat); ! } ! else { ! annots.addFeature(feat); ! } } ! else { ! processEvidence(feat); ! FeatureSetI []fsArray = resultSets.get(gff.getSource()); ! if (fsArray == null) { ! fsArray = new FeatureSet[2]; ! resultSets.put(gff.getSource(), fsArray); ! } ! int arrayIdx = gff.getStrand() == 1 ? 1 : 0; ! FeatureSetI fs = fsArray[arrayIdx]; ! if (fs == null) { ! fs = new FeatureSet(gff.getSource(), gff.getStrand()); ! fsArray[arrayIdx] = fs; ! } ! fs.addFeature(feat); /* ! results.addFeature(feat); */ } } } ! ! // add FeaturePair objects to any matches with no match_part children ! for (GFF3Data data : matches) { ! SeqFeatureI match = data.getFeat(); ! if (match.getFeatures().size() == 0) { ! GFF3Entry matchPart = new GFF3Entry(data.getEntry().toString()); ! matchPart.setType("match_part"); ! try { ! SeqFeatureI matchPartFeat = matchPart.createFeature(oboParser); ! processEvidence(matchPartFeat); ! match.addFeature(matchPartFeat); } ! catch (ClassNotFoundException e) { ! throw new ApolloAdapterException("Cannot locate Apollo datamodel class: " + e.getMessage()); } ! catch (IllegalAccessException e) { ! throw new ApolloAdapterException(e); ! } ! catch (InstantiationException e) { ! throw new ApolloAdapterException("Cannot instantiate class: " + e.getMessage()); } } } ! ! for (Map.Entry<String, FeatureSetI[]> e : resultSets.entrySet()) { ! if (e.getValue()[0] != null) { ! results.addFeature(e.getValue()[0]); } ! if (e.getValue()[1] != null) { ! results.addFeature(e.getValue()[1]); } } ! setTranslationEnds(gffMap, cdsCoords); } *************** *** 781,792 **** if (coords != null) { Transcript trans = (Transcript)feat; if (trans.getStrand() == -1) { ! trans.setTranslationStart(coords[1]); ! trans.setTranslationEnd(coords[0]); } ! else { ! trans.setTranslationStart(coords[0]); ! trans.setTranslationEnd(coords[1]); } } } --- 787,833 ---- if (coords != null) { Transcript trans = (Transcript)feat; + int stran = trans.getStart(); + int scds; + int ecds; + int fix; //used to fix stop codon Apollo uses the first base of + //the stop codon rather than the last base as translation end + + + //arrange CDS start and end by strand if (trans.getStrand() == -1) { ! scds = coords[1]; ! ecds = coords[0]; ! fix = 2; } ! else{ ! scds = coords[0]; ! ecds = coords[1]; ! fix = -2; ! } ! ! //only set start if CDS is real start_codon ! //or if CDS start and transcript start differ ! if(stran == scds){ ! String cod = trans.na2aa(trans.getRefSequence().getResidues(stran, stran + (fix * -1))); ! //String cod = trans.getStartAA(); ! if(cod.equals("M")){ ! trans.setTranslationStart(scds); ! } } + else{ + trans.setTranslationStart(scds); + } + + //let Apollo search for the end + //Check the last base againt the CDS end + //If different use the CDS from the GFF3 file + //This avoids forcing false stop codons + //and instead lets translations just stop + trans.setTranslationEndFromStart(); + int last = trans.getLastBaseOfStopCodon(); + if(last != ecds){ + trans.setTranslationEnd(ecds + fix); //fixed for first base of stop codon + } + } } *************** *** 869,873 **** throw new ApolloAdapterException("No valid Apollo OBO extension found"); } ! LinkedList<String> fnames = new LinkedList(); String soFile = IOUtil.findFile(so); String apolloFile = IOUtil.findFile(apollo); --- 910,914 ---- throw new ApolloAdapterException("No valid Apollo OBO extension found"); } ! LinkedList<String> fnames = new LinkedList<String>(); String soFile = IOUtil.findFile(so); String apolloFile = IOUtil.findFile(apollo); *************** *** 935,944 **** } } ! private static boolean isUrl(String fname) { return fname.contains("://"); } ! private static Reader getReader(String fname) throws IOException { --- 976,985 ---- } } ! private static boolean isUrl(String fname) { return fname.contains("://"); } ! private static Reader getReader(String fname) throws IOException { *************** *** 960,962 **** } ! } --- 1001,1003 ---- } ! } \ No newline at end of file Index: GFF3Entry.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gff3/GFF3Entry.java,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** GFF3Entry.java 8 Jun 2009 19:10:58 -0000 1.11 --- GFF3Entry.java 15 Jul 2009 20:34:44 -0000 1.12 *************** *** 25,28 **** --- 25,29 ---- private static Set<String> oneLevelAnnots; private static Set<String> threeLevelAnnots; + private static Set<String> reservedAttributes; private static int tmpIdCounter; static { *************** *** 36,39 **** --- 37,43 ---- "miRNA" })); + reservedAttributes = new TreeSet<String>(Arrays.asList(new String[] { + "ID", "Name", "Dbxref", "Ontology_term", "Gap", "Alias", "Target", "Note", "Parent" + })); tmpIdCounter = 0; } *************** *** 334,338 **** feat = javaClassName != null ? (SeqFeatureI)Class.forName(javaClassName).newInstance() : new AnnotatedFeature(); ! //new SeqFeature(); //Can't really handle match_part objects in a general way for dynamic class loading since --- 338,342 ---- feat = javaClassName != null ? (SeqFeatureI)Class.forName(javaClassName).newInstance() : new AnnotatedFeature(); ! //new SeqFeature(); //Can't really handle match_part objects in a general way for dynamic class loading since *************** *** 417,420 **** --- 421,440 ---- } } + + //non-GFF3 standard user defined attributes as feature properties + for (Map.Entry<String, List<String> > entry : attrs.entrySet()) { + if (isReservedAttribute(entry.getKey()) || entry.getKey().equals("Derives_from")) { + continue; + } + + String key = entry.getKey(); + List<String> values = entry.getValue(); + if (values != null) { + for (String value : values) { + feat.addProperty(key, value); + } + } + } + return feat; } *************** *** 544,605 **** src = feat.getProgramName() != null && feat.getProgramName().length() > 0 ? feat.getProgramName() : "."; ! type = feat.getFeatureType(); ! start = feat.getLow(); ! end = feat.getHigh(); ! score = feat.getScore(); ! strand = feat.getStrand(); ! phase = feat.getPhase(); ! id = feat.getId(); ! name = feat.getName(); ! //populate dbxrefs ! for (Object o : feat.getDbXrefs()) { ! DbXref dbxref = (DbXref)o; ! String key; ! String value; ! //if dbxref is an ontology ID or it contains ":", in which case ! //we assume it to be an ontology ID, don't prepend the database ! if (dbxref.isOntology() || dbxref.getIdValue().contains(":")) { ! key = "Ontology_term"; ! value = dbxref.getIdValue(); ! } ! else { ! key = "Dbxref"; ! value = dbxref.getDbName() + ":" + dbxref.getIdValue(); ! } ! addAttributeValue(key, value); ! } ! if (feat instanceof AnnotatedFeatureI) { ! AnnotatedFeatureI annot = (AnnotatedFeatureI)feat; ! //populate aliases ! for (Object o : annot.getSynonyms()) { ! Synonym syn = (Synonym)o; ! addAttributeValue("Alias", syn.getName()); ! } ! //store comments ! for (Object o : annot.getComments()) { ! Comment c = (Comment)o; ! addAttributeValue("Note", c.getText()); ! } ! } ! else if (feat instanceof FeaturePairI) { ! FeaturePairI fp = (FeaturePairI)feat; ! setScore(fp.getScore()); ! SeqFeatureI hit = fp.getHitFeature(); ! SequenceI hitSeq = hit.getHitFeature().getRefSequence(); ! String hitRefId = hitSeq != null ? hitSeq.getName() : ! hit.getProperty("refId"); ! if (hitRefId == null || hitRefId.length() == 0) { ! GFF3Adapter.logger.warn("No target id for hit on " + ! fp.getQueryFeature().getName() + " [" + ! hit.getLow() + ", " + hit.getHigh() + "]"); ! return; ! } ! addAttributeValue("Target", hitRefId + " " + hit.getLow() + " " + ! hit.getHigh() + " " + strandToString(hit.getStrand())); ! String cigar = fp.getCigar(); ! if (cigar != null && cigar.length() > 0) { ! addAttributeValue("Gap", cigar); ! } ! } } --- 564,643 ---- src = feat.getProgramName() != null && feat.getProgramName().length() > 0 ? feat.getProgramName() : "."; ! type = feat.getFeatureType(); ! start = feat.getLow(); ! end = feat.getHigh(); ! score = feat.getScore(); ! strand = feat.getStrand(); ! phase = feat.getPhase(); ! id = feat.getId(); ! name = feat.getName(); ! //populate dbxrefs ! for (Object o : feat.getDbXrefs()) { ! DbXref dbxref = (DbXref)o; ! String key; ! String value; ! ! //if dbxref is an ontology ID don't prepend the database ! if (dbxref.isOntology()) { ! key = "Ontology_term"; ! value = dbxref.getIdValue(); ! } ! else { ! key = "Dbxref"; ! value = dbxref.getDbName() + ":" + dbxref.getIdValue(); ! } ! addAttributeValue(key, value); ! } ! if (feat instanceof AnnotatedFeatureI) { ! AnnotatedFeatureI annot = (AnnotatedFeatureI)feat; ! //populate aliases ! for (Object o : annot.getSynonyms()) { ! Synonym syn = (Synonym)o; ! addAttributeValue("Alias", syn.getName()); ! } ! //store comments ! for (Object o : annot.getComments()) { ! Comment c = (Comment)o; ! addAttributeValue("Note", c.getText()); ! } ! } ! else if (feat instanceof FeaturePairI) { ! FeaturePairI fp = (FeaturePairI)feat; ! setScore(fp.getScore()); ! SeqFeatureI hit = fp.getHitFeature(); ! SequenceI hitSeq = hit.getHitFeature().getRefSequence(); ! String hitRefId = hitSeq != null ? hitSeq.getName() : ! hit.getProperty("refId"); ! if (hitRefId == null || hitRefId.length() == 0) { ! GFF3Adapter.logger.warn("No target id for hit on " + ! fp.getQueryFeature().getName() + " [" + ! hit.getLow() + ", " + hit.getHigh() + "]"); ! return; ! } ! addAttributeValue("Target", hitRefId + " " + hit.getLow() + " " + ! hit.getHigh() + " " + strandToString(hit.getStrand())); ! String cigar = fp.getCigar(); ! if (cigar != null && cigar.length() > 0) { ! addAttributeValue("Gap", cigar); ! } ! } ! ! //add other properties to attributes ! Hashtable hash = feat.getProperties(); ! for (Object o : hash.entrySet()) { ! Map.Entry<String, String> e = (Map.Entry<String, String>)o; ! String key = e.getKey(); ! String value = (String)e.getValue(); ! ! //key can not equal reserved attributes ! //also ignore program which is redundant with the source tag ! if (isReservedAttribute(key) || key.equals("program")) { ! continue; ! } ! ! if (value != null) { ! addAttributeValue(key, value); ! } ! } } *************** *** 641,651 **** ("Malformatted dbxref: " + dbxref); } - /* - feat.addDbXref(new DbXref("id", dbxref.substring(idx + 1), - dbxref.substring(0, idx), isOntology)); - */ feat.addDbXref(new DbXref("id", isOntology ? dbxref : dbxref.substring(idx + 1), ! dbxref.substring(0, idx), isOntology)); } } --- 679,685 ---- ("Malformatted dbxref: " + dbxref); } feat.addDbXref(new DbXref("id", isOntology ? dbxref : dbxref.substring(idx + 1), ! dbxref.substring(0, idx), isOntology)); } } *************** *** 673,680 **** return javaClassName; } ! private void setTmpId() { setId(String.format("ID%06d", ++tmpIdCounter)); } ! } --- 707,719 ---- return javaClassName; } ! private void setTmpId() { setId(String.format("ID%06d", ++tmpIdCounter)); } ! ! private boolean isReservedAttribute(String key) ! { ! return reservedAttributes.contains(key); ! } ! } \ No newline at end of file |
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From: elee <gk...@us...> - 2009-07-07 22:00:11
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Update of /cvsroot/gmod/apollo/src/java/apollo/config In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv12370 Modified Files: Style.java Log Message: + Removed unused and proprietary imports (which could cause a problem in the future) Index: Style.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/config/Style.java,v retrieving revision 1.63 retrieving revision 1.64 diff -C2 -d -r1.63 -r1.64 *** Style.java 5 Aug 2008 01:13:45 -0000 1.63 --- Style.java 7 Jul 2009 22:00:04 -0000 1.64 *************** *** 13,24 **** import java.io.FileWriter; import java.util.*; - import javax.swing.JOptionPane; - import javax.swing.text.html.HTMLDocument.HTMLReader.IsindexAction; import org.apache.log4j.*; - import org.bdgp.io.DataAdapterException; - import org.bdgp.io.DataAdapterRegistry; - - import com.sun.corba.se.spi.legacy.connection.GetEndPointInfoAgainException; import apollo.config.Config; --- 13,18 ---- *************** *** 26,30 **** import apollo.config.FeatureProperty; import apollo.config.PropertyScheme; - import apollo.util.IOUtil; /** A Style is basically config options for a particular data adapter */ --- 20,23 ---- |
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From: elee <gk...@us...> - 2009-07-07 18:28:33
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Update of /cvsroot/gmod/apollo/doc/release-notes In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv28958 Added Files: release-1.11.1-notes Log Message: + Release notes for release 1.11.1 --- NEW FILE: release-1.11.1-notes --- + Various bugfixes |
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From: elee <gk...@us...> - 2009-07-07 16:57:05
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