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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/organism ApolloNameAdapterI.java,1.12,1.13 DefaultNameAdapter.java,1.16,1.17 FlyNameAdapter.java,1.22,1.23 FlyOverlap.java,1.4,1.5 HumanOverlap.java,1.1,1.2
Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism
In directory sc8-pr-cvs1:/tmp/cvs-serv18105/apollo/dataadapter/organism
Modified Files:
ApolloNameAdapterI.java DefaultNameAdapter.java
FlyNameAdapter.java FlyOverlap.java HumanOverlap.java
Log Message:
This is a sizable commit, but still needs further debugging.
The biggest changes are the removal of GenericAnnotations, which
have been replaced by AnnotatedFeatures. These do what Mark has
long advocated: the FeatureSet is at the top and SeqFeatures
inherit from them. Didn't do it for everything, only annotated
features. This means that an Exon is now a 'set', but one that
can never have child features. I tried to find most of the bugs
due to set methods being called instead of the more appropriate
non-set methods, but there are likely still to be more lurking.
Be on the look-out for problems that might be called due to this
change. All-in-all I like this new way of doing things and think
we should consider it for all of the features. Another thing to
look out for is misinterpreted casting, since Gene as a class
is no longer there it takes actual code to determine if the
AnnotatedFeature is at the top or is a Transcript/Exon.
In addition fixed 2 small other bugs.
1. the annotation tree panel is up again
2. <ctrl>c and <ctrl>e no longer throw array out of bounds exception
Index: ApolloNameAdapterI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism/ApolloNameAdapterI.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** ApolloNameAdapterI.java 18 Dec 2003 17:33:09 -0000 1.12
--- ApolloNameAdapterI.java 31 Dec 2003 23:24:35 -0000 1.13
***************
*** 19,22 ****
--- 19,28 ----
public void setName(SeqFeatureI feature, String name);
+ // sets the name of a feature based upon its parent
+ public void setName(Transcript transcript, AnnotatedFeatureI gene);
+
+ // sets the name of a derived sequences based upon transcript name
+ public void changeSeqNames(Transcript transcript);
+
//find out if name is an id string
public boolean nameIsId (SeqFeatureI feature);
***************
*** 29,37 ****
//generates a name for a given feature
! public String selectMergeName(Gene feature1, Gene feature2);
//generates a URL
! //public String generateURL (Gene g);
! public String generateURL (GenericAnnotationI g);
// get the display name of a seqfeature
--- 35,43 ----
//generates a name for a given feature
! public String selectMergeName(AnnotatedFeatureI feature1,
! AnnotatedFeatureI feature2);
//generates a URL
! public String generateURL (AnnotatedFeatureI g);
// get the display name of a seqfeature
Index: DefaultNameAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism/DefaultNameAdapter.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** DefaultNameAdapter.java 20 Dec 2003 01:16:39 -0000 1.16
--- DefaultNameAdapter.java 31 Dec 2003 23:24:35 -0000 1.17
***************
*** 22,27 ****
//generates a name for a given feature
public String generateName(SeqFeatureI feature) {
! if (feature instanceof Gene) {
! return getName(Gene.class, geneNumber, "GN", "");
} else if (feature instanceof Transcript) {
return getName (Transcript.class, transcriptNumber, "XS", "");
--- 22,27 ----
//generates a name for a given feature
public String generateName(SeqFeatureI feature) {
! if (feature instanceof AnnotatedFeature) {
! return getName(AnnotatedFeature.class, geneNumber, "GN", "");
} else if (feature instanceof Transcript) {
return getName (Transcript.class, transcriptNumber, "XS", "");
***************
*** 34,39 ****
//generates a ID for a given feature
public String generateId(SeqFeatureI feature) {
! if (feature instanceof Gene) {
! return getId (Gene.class, geneNumber, "GN", "");
} else if (feature instanceof Transcript) {
return getId(Transcript.class, transcriptNumber, "XS", "");
--- 34,39 ----
//generates a ID for a given feature
public String generateId(SeqFeatureI feature) {
! if (feature instanceof AnnotatedFeature) {
! return getId (AnnotatedFeature.class, geneNumber, "GN", "");
} else if (feature instanceof Transcript) {
return getId(Transcript.class, transcriptNumber, "XS", "");
***************
*** 48,56 ****
}
//generates a ID for a given feature
public boolean nameIsId (SeqFeatureI feature) {
String prefix;
! if (feature instanceof Gene) {
prefix = "GN";
} else if (feature instanceof Transcript) {
--- 48,67 ----
}
+ public void setName(Transcript feature, AnnotatedFeatureI gene) {
+ feature.setName(gene.getName());
+ }
+
+ public void changeSeqNames(Transcript t) {
+ if (t.get_cDNASequence() != null)
+ t.get_cDNASequence().setAccessionNo(t.getName());
+ if (t.getPeptideSequence() != null) {
+ t.getPeptideSequence().setAccessionNo(t.getName());
+ }
+ }
//generates a ID for a given feature
public boolean nameIsId (SeqFeatureI feature) {
String prefix;
! if (feature instanceof AnnotatedFeature) {
prefix = "GN";
} else if (feature instanceof Transcript) {
***************
*** 119,123 ****
}
! public String generateURL (GenericAnnotationI g) {
return null;
}
--- 130,134 ----
}
! public String generateURL (AnnotatedFeatureI g) {
return null;
}
***************
*** 133,137 ****
}
! public String selectMergeName (Gene feature1, Gene feature2) {
String chosen_name = feature1.getName();
return chosen_name;
--- 144,149 ----
}
! public String selectMergeName (AnnotatedFeatureI feature1,
! AnnotatedFeatureI feature2) {
String chosen_name = feature1.getName();
return chosen_name;
***************
*** 144,155 ****
// This isn't terrible, but it seems like a waste of time.
// I'm not sure why it's getting called so much.
- // System.out.println("DefaultNameAdapter:getDisplayName: display_name = " + display_name + " for feature " + sf); // DEL
if (
display_name.equals(Range.NO_NAME) &&
! (sf instanceof FeatureSetI) &&
! ! (sf instanceof GenericAnnotationSet)
! ) {
FeatureSetI fs = (FeatureSetI) sf;
-
sf = fs.getFeatureAt(0);
display_name = fs.getFeatureAt(0).getName();
--- 156,163 ----
// This isn't terrible, but it seems like a waste of time.
// I'm not sure why it's getting called so much.
if (
display_name.equals(Range.NO_NAME) &&
! (sf instanceof FeatureSetI) && ! (sf instanceof AnnotatedFeatureI)) {
FeatureSetI fs = (FeatureSetI) sf;
sf = fs.getFeatureAt(0);
display_name = fs.getFeatureAt(0).getName();
***************
*** 200,204 ****
public String peptideName(String name) {
! return name; // Don't do anything to it (not sure if there should be a general rule)
}
--- 208,213 ----
public String peptideName(String name) {
! // Don't do anything to it (not sure if there should be a general rule)
! return name;
}
***************
*** 214,221 ****
if (sf instanceof ExonI) {
- // System.out.print("exon ");
ExonI exon = (ExonI)sf;
! if (exon.getTranscript() != null) {
! name = exon.getTranscript().getName();
} else {
System.out.println("WARNING: No transcript for exon " +
--- 223,229 ----
if (sf instanceof ExonI) {
ExonI exon = (ExonI)sf;
! if (exon.getRefFeature() != null) {
! name = exon.getRefFeature().getName();
} else {
System.out.println("WARNING: No transcript for exon " +
Index: FlyNameAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism/FlyNameAdapter.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** FlyNameAdapter.java 18 Dec 2003 17:33:09 -0000 1.22
--- FlyNameAdapter.java 31 Dec 2003 23:24:35 -0000 1.23
***************
*** 17,36 ****
/** Current format of dates in FASTA header lines for Drosophila, e.g.
! * >gi||gb|AB003910|AB003910 Fruitfly DNA for 88F actin, complete cds. (08-JUN-1999)
! * Should this format be defined in game.style? Or maybe we could figure out the
! * date format from the dates themselves?? */
! private static SimpleDateFormat dateFormat = new SimpleDateFormat("dd-MMM-yyyy");
!
!
! /** generates a name for a given feature - this only works for
! genes, transcripts and exons */
public String generateName(SeqFeatureI feature) {
! if (feature instanceof Gene) {
! return getGeneName((Gene) feature);
} else if (feature instanceof Transcript) {
return getTransName ((Transcript) feature);
! } else if (feature instanceof ExonI) {
! int num = getNameCount (ExonI.class, exonNumber, "EX");
! return "EX:temp"+(num);
} else
return "???";
--- 17,34 ----
/** Current format of dates in FASTA header lines for Drosophila, e.g.
! * >gi||gb|AB003910|AB003910 Fruitfly DNA for 88F actin, complete cds.
! * (08-JUN-1999)
! * Should this format be defined in game.style?
! * Or maybe we could figure out the date format from the dates themselves??
! * generates a name for a given feature - this only works for
! genes, transcripts and exons */
public String generateName(SeqFeatureI feature) {
! if (feature instanceof ExonI) {
! int num = getNameCount (ExonI.class, exonNumber, "EX");
! return "EX:temp"+(num);
} else if (feature instanceof Transcript) {
return getTransName ((Transcript) feature);
! } else if (feature instanceof AnnotatedFeature) {
! return getGeneName((AnnotatedFeature) feature);
} else
return "???";
***************
*** 39,54 ****
//generates a ID for a given feature
public String generateId(SeqFeatureI feature) {
! if (feature instanceof Gene) {
! if ((feature.getId() != null &&
! feature.getId().startsWith ("CR")) ||
! (feature.getName() != null &&
! feature.getName().startsWith("CR")))
! return getId (Gene.class, geneNumber, "CR", "");
! else
! return getId (Gene.class, geneNumber, "CG", "");
} else if (feature instanceof Transcript) {
return getId(Transcript.class, transcriptNumber, "CT", "");
! } else if (feature instanceof ExonI) {
! return getId(ExonI.class, exonNumber, "EX", "");
} else
return "???";
--- 37,52 ----
//generates a ID for a given feature
public String generateId(SeqFeatureI feature) {
! if (feature instanceof ExonI) {
! return getId(ExonI.class, exonNumber, "EX", "");
} else if (feature instanceof Transcript) {
return getId(Transcript.class, transcriptNumber, "CT", "");
! } else if (feature instanceof AnnotatedFeature) {
! if ((feature.getId() != null &&
! feature.getId().startsWith ("CR")) ||
! (feature.getName() != null &&
! feature.getName().startsWith("CR")))
! return getId (AnnotatedFeature.class, geneNumber, "CR", "");
! else
! return getId (AnnotatedFeature.class, geneNumber, "CG", "");
} else
return "???";
***************
*** 56,103 ****
public String getDisplayName (SeqFeatureI sf) {
! // System.out.println("FNA.getDisplayName: getting name for " + sf.getClass().getName() + " " + sf.getName()); // DEL
! return sf.getName();
}
! // This is used for making labels in the display. The result names are too long,
! // e.g. AY058300-AE003603.Sept-na_gb.dros, when what we want is just AY085300.
! // !! I'd like the labels to look like the names made by SetDetailPanel.setupHeader
! // but can't just directly use that method, because it has access to a FeatureSet
! // as well as a SeqFeature. Need to make this work.
! // For now, using a kludge to shorten the names.
public String getShortName (SeqFeatureI sf) {
String name = getDisplayName(sf);
- // Not working right
- // if (sf instanceof FeaturePair) {
- // // SequenceI seq = fset.getAlignmentSequence();
- // SeqFeatureI hit = ((FeaturePair)sf).getHitFeature();
- // SequenceI seq = hit.getRefSequence();
- // System.out.println("getShortName(" + name + "): hit = " + hit + ", seq = " + seq); // DEL
- // if (seq == null) {
- // seq = ((FeaturePair)sf).getRefSequence();
- // }
- // if (seq != null) {
- // name = seq.getDisplayId() != null ? seq.getDisplayId() : "";
- // } else {
- // name = hit.getName() != null ? hit.getName() : "";
- // }
- // }
- // else {
- // SequenceI seq = sf.getRefSequence();
- // SeqFeatureI feat = sf.getRefFeature();
- // System.out.println("getShortName(" + name + "): seq = " + seq); // DEL
- // if (seq == null) {
- // seq = feat.getRefSequence();
- // System.out.println("getShortName(" + name + "): ref feature = " + feat + ", seq = " + seq); // DEL
- // }
- // if (seq != null) {
- // name = seq.getDisplayId() != null ? seq.getDisplayId() : "";
- // } else {
- // name = feat.getName() != null ? feat.getName() : "";
- // }
- // }
-
- // This is a kludge to make the name shorter by chopping off unnecessary pieces
if (name.length() > 12) {
if (name.indexOf("-") > 5)
--- 54,78 ----
public String getDisplayName (SeqFeatureI sf) {
! if (sf instanceof ExonI) {
! Transcript transcript = ((ExonI) sf).getTranscript();
! return (transcript.getName() +
! " exon " + (transcript.getFeatureIndex(sf) + 1));
! }
! else
! return sf.getName();
}
! /** This is used for making labels in the display.
! The result names are too long,
! e.g. AY058300-AE003603.Sept-na_gb.dros, when what we want is
! just AY085300.
! !! I'd like the labels to look like the names made by
! SetDetailPanel.setupHeader
! but can't just directly use that method, because it has access
! to a FeatureSet as well as a SeqFeature. Need to make this work.
! For now, using a kludge to shorten the names. */
public String getShortName (SeqFeatureI sf) {
String name = getDisplayName(sf);
if (name.length() > 12) {
if (name.indexOf("-") > 5)
***************
*** 115,128 ****
name = name.substring(0, name.lastIndexOf("-"));
}
-
- // System.out.println("getShortName: short name for " + getDisplayName(sf) + " is " + name); // DEL
return name;
}
public void setName (SeqFeatureI sf, String name) {
! if (sf instanceof Gene) {
if ((name.startsWith("CR")) || (name.startsWith("CG"))) {
if ((sf.getId() != null) && (!sf.getId().equals(name))) {
! ((Gene) sf).addSynonym(sf.getId());
}
sf.setId(name);
--- 90,101 ----
name = name.substring(0, name.lastIndexOf("-"));
}
return name;
}
public void setName (SeqFeatureI sf, String name) {
! if (!(sf instanceof Transcript) && !(sf instanceof ExonI)){
if ((name.startsWith("CR")) || (name.startsWith("CG"))) {
if ((sf.getId() != null) && (!sf.getId().equals(name))) {
! ((AnnotatedFeatureI) sf).addSynonym(sf.getId());
}
sf.setId(name);
***************
*** 135,143 ****
public String getHeader (SeqFeatureI sf) {
if (sf instanceof FeaturePair) {
- // System.out.println("display id for " + sf + " (class " + sf.getClass().getName() + ") is " + ((FeaturePair)sf).getDisplayId()); // DEL
return ((FeaturePair)sf).getDisplayId();
} else {
! // System.out.println("display name for " + sf + " (class " + sf.getClass().getName() + ") is " + sf.getName()); // DEL
! return sf.getName();
}
}
--- 108,114 ----
public String getHeader (SeqFeatureI sf) {
if (sf instanceof FeaturePair) {
return ((FeaturePair)sf).getDisplayId();
} else {
! return getDisplayName(sf);
}
}
***************
*** 147,157 ****
String prefix;
boolean is_ID = false;
! if (feature instanceof Gene) {
! prefix = "CG";
is_ID = (getCG (feature.getName(), prefix) != null ||
feature.getName().startsWith (prefix+":temp") ||
(feature.getName().startsWith (prefix) &&
feature.getName().indexOf ("tmp") > 0));
! prefix = "CR";
} else if (feature instanceof Transcript) {
prefix = "CT";
--- 118,128 ----
String prefix;
boolean is_ID = false;
! if (feature instanceof ExonI) {
! prefix = "EX";
is_ID = (getCG (feature.getName(), prefix) != null ||
feature.getName().startsWith (prefix+":temp") ||
(feature.getName().startsWith (prefix) &&
feature.getName().indexOf ("tmp") > 0));
! prefix = "CG";
} else if (feature instanceof Transcript) {
prefix = "CT";
***************
*** 161,171 ****
feature.getName().indexOf ("tmp") > 0));
prefix = "CG";
! } else if (feature instanceof ExonI) {
! prefix = "EX";
is_ID = (getCG (feature.getName(), prefix) != null ||
feature.getName().startsWith (prefix+":temp") ||
(feature.getName().startsWith (prefix) &&
feature.getName().indexOf ("tmp") > 0));
! prefix = "CG";
} else
prefix = "???";
--- 132,142 ----
feature.getName().indexOf ("tmp") > 0));
prefix = "CG";
! } else if (feature instanceof AnnotatedFeature) {
! prefix = "CG";
is_ID = (getCG (feature.getName(), prefix) != null ||
feature.getName().startsWith (prefix+":temp") ||
(feature.getName().startsWith (prefix) &&
feature.getName().indexOf ("tmp") > 0));
! prefix = "CR";
} else
prefix = "???";
***************
*** 184,190 ****
prefix = prefix + ":temp";
Vector features
! = SeqFeatureUtil.getFeaturesOfClass(curationSet.getAnnots(),
! featureClass,
! false);
int num = start;
for(int i=0; i < features.size(); i++) {
--- 155,161 ----
prefix = prefix + ":temp";
Vector features
! = SeqFeatureUtil.getFeaturesOfClass(curationSet.getAnnots(),
! featureClass,
! false);
int num = start;
for(int i=0; i < features.size(); i++) {
***************
*** 210,275 ****
int start,
String prefix) {
! Vector features
! = SeqFeatureUtil.getFeaturesOfClass(curationSet.getAnnots(),
! featureClass,
! false);
! int num = start;
! for(int i=0; i < features.size(); i++) {
! SeqFeatureI g = (SeqFeatureI) features.elementAt(i);
! String this_name = g.getName();
! if (this_name.startsWith(prefix)) {
! try {
! // check for any temp in the name
! int index = this_name.indexOf (":temp");
! String num_str;
! // then parse out the count from the name
! if (index > 0)
! num_str = this_name.substring (index + ":temp".length());
! else {
! index = this_name.indexOf (":");
! if (index > 0)
! num_str = this_name.substring (index + 1);
! else
! num_str = this_name.substring(prefix.length());
! }
! // System.out.println ("Checking " + num_str +
! // " in " + this_name);
! int namenum = Integer.parseInt(num_str);
! if (namenum >= num) {
! num = namenum + 1;
! }
! } catch (NumberFormatException e) {}
! }
}
! return num;
}
! private String getGeneName (Gene feature) {
! String gene_name = feature.getName();
! if (gene_name.equals (SeqFeatureI.NO_NAME) ||
! gene_name.startsWith ("CG"))
! return getId (Gene.class, geneNumber, "CG", "");
! else if (gene_name.startsWith ("CR"))
! return getId (Gene.class, geneNumber, "CR", "");
! else {
! int index = gene_name.lastIndexOf (":");
! if (index > 0 && (index + 1) < gene_name.length()) {
! // then parse out the count from the name
! String num_str = gene_name.substring(index + 1);
! try {
! int namenum = Integer.parseInt(num_str);
! gene_name = gene_name.substring (0, index);
! // System.out.println ("Gene prefix is " + gene_name);
! } catch (NumberFormatException e) {}
! }
! int num = getNameCount (Gene.class, 1, gene_name);
! return gene_name+":"+(num);
! }
}
private String getTransName (Transcript feature) {
! Gene gene = feature.getGene();
! Vector transcripts = gene.getTranscripts();
int t_index = transcripts.indexOf (feature);
String new_name;
--- 181,245 ----
int start,
String prefix) {
! Vector features
! = SeqFeatureUtil.getFeaturesOfClass(curationSet.getAnnots(),
! featureClass,
! false);
! int num = start;
! for(int i=0; i < features.size(); i++) {
! SeqFeatureI g = (SeqFeatureI) features.elementAt(i);
! String this_name = g.getName();
! if (this_name.startsWith(prefix)) {
! try {
! // check for any temp in the name
! int index = this_name.indexOf (":temp");
! String num_str;
! // then parse out the count from the name
! if (index > 0)
! num_str = this_name.substring (index + ":temp".length());
! else {
! index = this_name.indexOf (":");
! if (index > 0)
! num_str = this_name.substring (index + 1);
! else
! num_str = this_name.substring(prefix.length());
! }
! // System.out.println ("Checking " + num_str +
! // " in " + this_name);
! int namenum = Integer.parseInt(num_str);
! if (namenum >= num) {
! num = namenum + 1;
! }
! } catch (NumberFormatException e) {}
}
! }
! return num;
}
! private String getGeneName (AnnotatedFeatureI feature) {
! String gene_name = feature.getName();
! if (gene_name.equals (SeqFeatureI.NO_NAME) ||
! gene_name.startsWith ("CG"))
! return getId (AnnotatedFeature.class, geneNumber, "CG", "");
! else if (gene_name.startsWith ("CR"))
! return getId (AnnotatedFeature.class, geneNumber, "CR", "");
! else {
! int index = gene_name.lastIndexOf (":");
! if (index > 0 && (index + 1) < gene_name.length()) {
! // then parse out the count from the name
! String num_str = gene_name.substring(index + 1);
! try {
! int namenum = Integer.parseInt(num_str);
! gene_name = gene_name.substring (0, index);
! } catch (NumberFormatException e) {}
! }
! int num = getNameCount (AnnotatedFeature.class, 1, gene_name);
! return gene_name+":"+(num);
}
+ }
private String getTransName (Transcript feature) {
! AnnotatedFeatureI gene = feature.getGene();
! Vector transcripts = gene.getFeatures();
int t_index = transcripts.indexOf (feature);
String new_name;
***************
*** 289,292 ****
--- 259,308 ----
}
+ /* 12/08/2003:
+ Transcript names (symbols) should inherit from parent annotation symbol,
+ not parent annotation ID.
+ Transcript ID (passed as argument) is used only for its *suffix*--
+ prefix is ignored. */
+ public void setName(Transcript t, AnnotatedFeatureI gene) {
+ // And what if it isn't? Then what??
+ String transcript_name;
+ String transcript_id = t.getId();
+ int index = (transcript_id != null ?
+ transcript_id.lastIndexOf("-") : -1);
+ if (index > 0) {
+ transcript_name=(gene.getName() + transcript_id.substring(index));
+ }
+ else {
+ transcript_name=(gene.getName() +
+ getNewSuffix(gene.getFeatureIndex(t),
+ gene.getFeatures()));
+ }
+ if (t.getName() == null ||
+ (t.getName() != null && !t.getName().equals(transcript_name))) {
+ t.setName(transcript_name);
+ // When transcript name is changed, change cDNA and peptide names also
+ changeSeqNames(t);
+ }
+ }
+
+ // Set the cDNA *and* peptide names based on the new transcript name.
+ public void changeSeqNames(Transcript t) {
+ if (t.get_cDNASequence() != null)
+ t.get_cDNASequence().setAccessionNo(t.getName());
+ if (t.getPeptideSequence() != null) {
+ t.getPeptideSequence().setAccessionNo(peptideName(t.getName()));
+ }
+ }
+
+ // Convert a cdna name to a peptide name by changing -R to -P, e.g.
+ // CG123-RA -> CG123-PA
+ public String peptideName(String name) {
+ if (name.indexOf("-R") > 0) {
+ name = name.substring(0, name.indexOf("-R")+1) + "P" +
+ name.substring(name.indexOf("-R") + 2);
+ }
+ return name;
+ }
+
// Construct a new index for transcript #t_index, following the
// pattern -RA, -RB, ..., -RAA, -RAB, ... -RZZ
***************
*** 301,315 ****
letter = (char)('A' + div26);
suffix = suffix + letter;
- // System.out.println("t_index > 26. t_index = " + t_index + ", div26 = " + div26 + ", letter = " + letter + ", suffix = " + suffix);
}
int remainder = t_index % 26;
letter = (char)('A' + remainder);
suffix = suffix + letter;
- // System.out.println("Out of loop, num transcripts = " + transcripts.size() + ", t_index = " + t_index + ", remainder = " + remainder + ", letter = " + letter + ", now suffix = " + suffix);
-
suffix = "-R" + suffix;
// make sure it is unique
if (suffixInUse (transcripts, suffix, t_index)) {
- // System.out.println("Suffix in use: " + suffix + "--recursively calling getNewSuffix(" + t_index +"+1)");
// If that suffix was used, recursively choose a new one.
return(getNewSuffix(t_index+1, transcripts));
--- 317,327 ----
***************
*** 318,322 ****
}
! public String generateURL (GenericAnnotationI g) {
Hashtable id_hash = new Hashtable();
--- 330,334 ----
}
! public String generateURL (AnnotatedFeatureI g) {
Hashtable id_hash = new Hashtable();
***************
*** 342,348 ****
id_hash.put (id, id);
else {
! id = getCG ((String) g.getSynonyms().elementAt(i), "CR");
! if (id != null)
! id_hash.put (id, id);
}
}
--- 354,360 ----
id_hash.put (id, id);
else {
! id = getCG ((String) g.getSynonyms().elementAt(i), "CR");
! if (id != null)
! id_hash.put (id, id);
}
}
***************
*** 352,358 ****
id_hash.put (id, id);
else {
! id = getCG (g.getName(), "CR");
! if (id != null)
! id_hash.put (id, id);
}
--- 364,370 ----
id_hash.put (id, id);
else {
! id = getCG (g.getName(), "CR");
! if (id != null)
! id_hash.put (id, id);
}
***************
*** 361,371 ****
id_hash.put (id, id);
else {
! id = getCG (g.getId(), "CR");
! if (id != null)
! id_hash.put (id, id);
}
! // The code here was glomming together all the elements into one big |ed string,
! // but that's not what the gene report CGI wants. An FBgn or CG should be sufficient.
StringBuffer query_str = new StringBuffer();
for (Enumeration e = id_hash.elements() ;
--- 373,384 ----
id_hash.put (id, id);
else {
! id = getCG (g.getId(), "CR");
! if (id != null)
! id_hash.put (id, id);
}
! // The code here was glomming together all the elements into one
! // big |ed string, but that's not what the gene report CGI wants.
! // An FBgn or CG should be sufficient.
StringBuffer query_str = new StringBuffer();
for (Enumeration e = id_hash.elements() ;
***************
*** 432,467 ****
}
! public String selectMergeName (Gene feature1, Gene feature2) {
! String chosen_name = feature1.getName();
! String name1 = feature1.getName();
! String name2 = feature2.getName();
! if (name1.equals (SeqFeatureI.NO_NAME))
! name1 = "CG";
! if (name2.equals (SeqFeatureI.NO_NAME))
! name2 = "CG";
! // If one of them has "temp" in its name, that is never the right choice--
! // pick the other one.
! if (name2.indexOf (":temp") >= 0)
! return name1;
! else if (name1.indexOf (":temp") >= 0)
! return name2;
! if ((name1.startsWith ("CG") && name2.startsWith ("CG")) ||
! (name1.startsWith ("CG") && name2.startsWith ("CR")) ||
! (name1.startsWith ("CR") && name2.startsWith ("CG"))) {
! chosen_name = getId (Gene.class, geneNumber, "CG", "");
! }
! else if (name1.startsWith ("CR") && name2.startsWith ("CR")) {
! chosen_name = getId (Gene.class, geneNumber, "CR", "");
! }
! else if (name1.startsWith ("CG") || name1.startsWith("CR")) {
! chosen_name = name2;
! }
! else if (name2.startsWith ("CG") || name2.startsWith("CR")) {
! chosen_name = name1;
! }
! else {
// Cambridge has to decide these based on date
// precedence (Can this be inferred from FBgn?)
--- 445,481 ----
}
! public String selectMergeName (AnnotatedFeatureI feature1,
! AnnotatedFeatureI feature2) {
! String chosen_name = feature1.getName();
! String name1 = feature1.getName();
! String name2 = feature2.getName();
! if (name1.equals (SeqFeatureI.NO_NAME))
! name1 = "CG";
! if (name2.equals (SeqFeatureI.NO_NAME))
! name2 = "CG";
! // If one of them has "temp" in its name, that is never the right choice--
! // pick the other one.
! if (name2.indexOf (":temp") >= 0)
! return name1;
! else if (name1.indexOf (":temp") >= 0)
! return name2;
! if ((name1.startsWith ("CG") && name2.startsWith ("CG")) ||
! (name1.startsWith ("CG") && name2.startsWith ("CR")) ||
! (name1.startsWith ("CR") && name2.startsWith ("CG"))) {
! chosen_name = getId (AnnotatedFeature.class, geneNumber, "CG", "");
! }
! else if (name1.startsWith ("CR") && name2.startsWith ("CR")) {
! chosen_name = getId (AnnotatedFeature.class, geneNumber, "CR", "");
! }
! else if (name1.startsWith ("CG") || name1.startsWith("CR")) {
! chosen_name = name2;
! }
! else if (name2.startsWith ("CG") || name2.startsWith("CR")) {
! chosen_name = name1;
! }
! else {
// Cambridge has to decide these based on date
// precedence (Can this be inferred from FBgn?)
***************
*** 473,477 ****
String id1 = xref1.getIdValue();
String id2 = xref1.getIdValue();
! if (id1 != null && id2 != null && id1.startsWith ("FBgn") && id2.startsWith ("FBgn")) {
id1 = id1.substring ("FBgn".length());
id2 = id2.substring ("FBgn".length());
--- 487,494 ----
String id1 = xref1.getIdValue();
String id2 = xref1.getIdValue();
! if (id1 != null &&
! id2 != null &&
! id1.startsWith ("FBgn") &&
! id2.startsWith ("FBgn")) {
id1 = id1.substring ("FBgn".length());
id2 = id2.substring ("FBgn".length());
***************
*** 510,524 ****
public String getBioTypeForDisplay(SeqFeatureI sf) {
- // String type = sf.getBioType();
- // // capitalize it
- // type = capitalize(type);
- // if (!type.equalsIgnoreCase("Transcript")) return type;
- // String parentType = sf.getRefFeature().getType();
- // // should this be Gene type?
- // if (parentType.equalsIgnoreCase("gene")) return type;
- // if (!parentType.equalsIgnoreCase("tRNA")) parentType = capitalize(parentType);
- // // should it just be parentType?
- // return parentType + " " + type;
-
String typeDisplay = sf.getBioType();
typeDisplay = capitalize(typeDisplay);
--- 527,530 ----
***************
*** 536,554 ****
}
! // Convert a cdna name to a peptide name by changing -R to -P, e.g.
! // CG123-RA -> CG123-PA
! public String peptideName(String name) {
! if (name.indexOf("-R") > 0) {
! // System.out.println("peptideName: changing " + name + " to "); // DEL
! name = name.substring(0, name.indexOf("-R")+1) + "P" + name.substring(name.indexOf("-R") + 2);
! // System.out.println(" " + name); // DEL
! }
! return name;
! }
!
! // Given a FASTA-style header line, extract the date.
! // For fly sequences, the expected format of the header line is
! // >gi||gb|AB003910|AB003910 Fruitfly DNA for 88F actin, complete cds. (08-JUN-1999)
! // Date is that thing at the end, obviously.
public Date getDateFromHeader(String header) {
Date date = null;
--- 542,559 ----
}
! /** Given a FASTA-style header line, extract the date.
! * For fly sequences, the expected format of the header line is
! * >gi||gb|AB003910|AB003910 Fruitfly DNA for 88F actin, complete cds.
! * (08-JUN-1999)
! * Date is that thing at the end, obviously.
! * Using the expected dateFormat (defined near the top of this file)
! * parse the date string and return it as a Date object.
! * People need to educate themselves about what is already available
! * in the code and stop reinventing things. Apollo will be impossible
! * to maintain otherwise. Look around first and either reuse existing
! * coding or consilidate common bits before re-writing anything.
! * I changed this to use Apollo.util.DateUtil SUZ
! */
!
public Date getDateFromHeader(String header) {
Date date = null;
***************
*** 562,589 ****
if (possibleDate.indexOf(")") >= 0)
possibleDate = possibleDate.substring(0, possibleDate.indexOf(")"));
! date = parseDate(possibleDate);
}
return date;
}
- /** Using the expected dateFormat (defined near the top of this file)
- * parse the date string and return it as a Date object. */
- public Date parseDate(String dateString) {
- try {
- Date date = dateFormat.parse(dateString);
- // System.out.println("Style.parseDate: parsed dateString " + dateString + ": " + date); // DEL
- return date;
- }
- catch (Exception e) {
- // System.out.println("Style.parseDate: couldn't parse date string " + dateString + ": " + e); // DEL
- return null;
- }
- }
-
// Returns true if the date in the description is newer than date2.
public boolean isNewerThan(String description, Date date2) {
Date date1 = getDateFromHeader(description);
- // System.out.println("FlyNameAdapter.isNewerThan(" + description + ", " + date2 + ") = " +
- // isNewerThan(date1, date2)); // DEL
return(isNewerThan(date1, date2));
}
--- 567,578 ----
if (possibleDate.indexOf(")") >= 0)
possibleDate = possibleDate.substring(0, possibleDate.indexOf(")"));
! date = DateUtil.makeADate(possibleDate);
}
return date;
}
// Returns true if the date in the description is newer than date2.
public boolean isNewerThan(String description, Date date2) {
Date date1 = getDateFromHeader(description);
return(isNewerThan(date1, date2));
}
***************
*** 593,604 ****
if (date1 == null || date2 == null)
return false;
! return (date2.compareTo(date1) <= 0);
! }
!
! /** The opposite of parseDate: converts a Date object to a String in
! * the current format. (This is needed in case the user wants to change the
! * tiers and save as a tiers file.) */
! public String formatDate(Date date) {
! return dateFormat.format(date);
}
--- 582,587 ----
if (date1 == null || date2 == null)
return false;
! else
! return (date2.compareTo(date1) <= 0);
}
Index: FlyOverlap.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism/FlyOverlap.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** FlyOverlap.java 5 Dec 2003 22:34:45 -0000 1.4
--- FlyOverlap.java 31 Dec 2003 23:24:35 -0000 1.5
***************
*** 14,18 ****
public boolean areOverlapping(SeqFeatureI sa,SeqFeatureI sb) {
boolean overlap = false;
! if (sb instanceof FeatureSetI) {
FeatureSetI fb = (FeatureSetI)sb;
for (int i=0; i<fb.size() && !overlap; i++) {
--- 14,18 ----
public boolean areOverlapping(SeqFeatureI sa,SeqFeatureI sb) {
boolean overlap = false;
! if (sb.canHaveChildren()) {
FeatureSetI fb = (FeatureSetI)sb;
for (int i=0; i<fb.size() && !overlap; i++) {
***************
*** 20,24 ****
}
}
! else if (sa instanceof FeatureSetI) {
FeatureSetI fa = (FeatureSetI)sa;
for (int i=0; i<fa.size() && !overlap; i++) {
--- 20,24 ----
}
}
! else if (sa.canHaveChildren()) {
FeatureSetI fa = (FeatureSetI)sa;
for (int i=0; i<fa.size() && !overlap; i++) {
Index: HumanOverlap.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/organism/HumanOverlap.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** HumanOverlap.java 23 Nov 2002 16:18:22 -0000 1.1
--- HumanOverlap.java 31 Dec 2003 23:24:35 -0000 1.2
***************
*** 18,22 ****
public boolean areOverlapping(SeqFeatureI sa,SeqFeatureI sb) {
boolean overlap = false;
! if (sb instanceof FeatureSetI) {
FeatureSetI fb = (FeatureSetI)sb;
for (int i=0; i<fb.size() && !overlap; i++) {
--- 18,22 ----
public boolean areOverlapping(SeqFeatureI sa,SeqFeatureI sb) {
boolean overlap = false;
! if (sb.canHaveChildren()) {
FeatureSetI fb = (FeatureSetI)sb;
for (int i=0; i<fb.size() && !overlap; i++) {
***************
*** 24,28 ****
}
}
! else if (sa instanceof FeatureSetI) {
FeatureSetI fa = (FeatureSetI)sa;
for (int i=0; i<fa.size() && !overlap; i++) {
--- 24,28 ----
}
}
! else if (sa.canHaveChildren()) {
FeatureSetI fa = (FeatureSetI)sa;
for (int i=0; i<fa.size() && !overlap; i++) {
|