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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui ApolloFrame.java,1.70.2.52,1.70.2.53 FeatureEditorDialog.java,1.15.2.19,1.15.2.20 FeatureTreePanel.java,1.39.2.9,1.39.2.10 GeneEditPanel.java,1.1.2.1,1.1.2.2 MouseManager.java,1.1.2.2,1.1.2.3 Selection.java,1.16.2.6,1.16.2.7 SelectionManager.java,1.1.2.4,1.1.2.5 TablePanel.java,1.4.2.7,1.4.2.8
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From: Mark G. <mg...@us...> - 2002-05-30 23:48:39
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Update of /cvsroot/gmod/apollo/src/java/apollo/gui
In directory usw-pr-cvs1:/tmp/cvs-serv24307
Modified Files:
Tag: sanger_branch
ApolloFrame.java FeatureEditorDialog.java
FeatureTreePanel.java GeneEditPanel.java MouseManager.java
Selection.java SelectionManager.java TablePanel.java
Log Message:
Selection coordination with annot info at the transcript level now working.
Index: ApolloFrame.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/ApolloFrame.java,v
retrieving revision 1.70.2.52
retrieving revision 1.70.2.53
diff -C2 -d -r1.70.2.52 -r1.70.2.53
*** ApolloFrame.java 30 May 2002 19:03:10 -0000 1.70.2.52
--- ApolloFrame.java 30 May 2002 23:48:35 -0000 1.70.2.53
***************
*** 265,268 ****
--- 265,269 ----
szap = new StrandedZoomableApolloPanel (true,true,controller);
selectionManager = new SelectionManager();
+ selectionManager.setController(controller); // for now
szap.getApolloPanel().setSelectionManager(selectionManager);
ftp.setSelectionManager(selectionManager);
Index: FeatureEditorDialog.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/FeatureEditorDialog.java,v
retrieving revision 1.15.2.19
retrieving revision 1.15.2.20
diff -C2 -d -r1.15.2.19 -r1.15.2.20
*** FeatureEditorDialog.java 30 May 2002 01:34:58 -0000 1.15.2.19
--- FeatureEditorDialog.java 30 May 2002 23:48:35 -0000 1.15.2.20
***************
*** 120,126 ****
setTitle(in.getName() + " Annotation Information");
// setListData triggers unneeded selection event
! dontFireSelection = true;
genePanel.setListData (annots, in);
! dontFireSelection = false;
// loadTranscript ();
}
--- 120,126 ----
setTitle(in.getName() + " Annotation Information");
// setListData triggers unneeded selection event
! //dontFireSelection = true;
genePanel.setListData (annots, in);
! //dontFireSelection = false;
// loadTranscript ();
}
***************
*** 129,134 ****
--- 129,136 ----
public void loadTranscript () {
Gene clone = (Gene) genePanel.getSelectedFeature();
+ //dontFireSelection = true;
transcriptPanel.setListData(clone.getFeatures(),
(GenericAnnotationSetI) clone.getFeatureAt (0));
+ //dontFireSelection = false;
}
***************
*** 490,499 ****
selectionManager = sm;
JList featList = transcriptPanel.getFeatureList();
featList.addListSelectionListener(new ListSelectionListener() {
public void valueChanged(ListSelectionEvent e) {
if (dontFireSelection || e.getValueIsAdjusting()) return;
! JList featList = transcriptPanel.getFeatureList();
! SeqFeatureI feat = (SeqFeatureI)featList.getSelectedValue();
! if (feat != null) selectionManager.select(feat);
} } );
}
--- 492,505 ----
selectionManager = sm;
JList featList = transcriptPanel.getFeatureList();
+ //JList featList = genePanel.getFeatureList();
featList.addListSelectionListener(new ListSelectionListener() {
public void valueChanged(ListSelectionEvent e) {
if (dontFireSelection || e.getValueIsAdjusting()) return;
! JList tranList = transcriptPanel.getFeatureList();
! //JList featList = genePanel.getFeatureList();
! Transcript clone = (Transcript)tranList.getSelectedValue();
! Transcript real_tran = genePanel.cloneToRealTranscript(clone);
! if (real_tran != null)
! selectionManager.select(real_tran,FeatureEditorDialog.this);
} } );
}
***************
*** 530,533 ****
--- 536,540 ----
evt.getSource() != this &&
evt.getFeatures().size() > 0) {
+ dontFireSelection = true;
SeqFeatureI sf = (SeqFeatureI)evt.getFeatures().elementAt(0);
Gene previous_gene = annot;
***************
*** 536,540 ****
--- 543,557 ----
loadGUI(annot);
}
+ if (sf instanceof Transcript) {
+ Transcript clone = genePanel.realToCloneTranscript((Transcript)sf);
+ transcriptPanel.featureList.setSelectedValue(clone,true);
+ }
+ else if (sf instanceof Exon) {
+ Transcript t = (Transcript)sf.getRefFeature();
+ Transcript clone = genePanel.realToCloneTranscript(t);
+ transcriptPanel.featureList.setSelectedValue(clone,true);
+ }
}
+ dontFireSelection = false;
return false;
}
Index: FeatureTreePanel.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/FeatureTreePanel.java,v
retrieving revision 1.39.2.9
retrieving revision 1.39.2.10
diff -C2 -d -r1.39.2.9 -r1.39.2.10
*** FeatureTreePanel.java 29 May 2002 01:48:16 -0000 1.39.2.9
--- FeatureTreePanel.java 30 May 2002 23:48:35 -0000 1.39.2.10
***************
*** 369,373 ****
}
//controller.handleFeatureSelectionEvent(new FeatureSelectionEvent(this,sf));
! selectionManager.select(sf);
}
--- 369,373 ----
}
//controller.handleFeatureSelectionEvent(new FeatureSelectionEvent(this,sf));
! selectionManager.select(sf,this);
}
Index: GeneEditPanel.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/Attic/GeneEditPanel.java,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** GeneEditPanel.java 6 May 2002 14:43:46 -0000 1.1.2.1
--- GeneEditPanel.java 30 May 2002 23:48:35 -0000 1.1.2.2
***************
*** 11,14 ****
--- 11,15 ----
import java.util.Hashtable;
import java.util.Enumeration;
+ import com.sun.java.util.collections.HashMap;
import java.io.IOException;
***************
*** 30,33 ****
--- 31,38 ----
public class GeneEditPanel extends FeatureEditPanel {
+ /** Table size should perhaps be higher than 32 which is just one row,
+ at the moment there is only one row of data */
+ private static final Dimension tableSize = new Dimension(400,32);
+
ReadWriteField featureTypeList = new ReadWriteField(true);
JTextArea bigCommentField = new JTextArea(10,3);
***************
*** 41,47 ****
private DbxRefTableModel model; // dbxref table model
! /** Table size should perhaps be higher than 32 which is just one row,
! at the moment there is only one row of data */
! private static final Dimension tableSize = new Dimension(400,32);
public GeneEditPanel(FeatureEditorDialog frame,
--- 46,54 ----
private DbxRefTableModel model; // dbxref table model
!
! /** Map cloned transcripts back to their real transcript which is needed for
! * selection event */
! private HashMap cloneToRealTranscriptHash = new HashMap();
! private HashMap realToCloneTranscriptHash = new HashMap();
public GeneEditPanel(FeatureEditorDialog frame,
***************
*** 371,374 ****
--- 378,384 ----
out.setIsProblematic(in.isProblematic());
out.setType(in.getType());
+ // Start and end needed for equality for sending out clone in selection
+ out.setStart(in.getStart());
+ out.setEnd(in.getEnd());
for(int i=0; i < in.getComments().size(); i++)
***************
*** 385,390 ****
--- 395,410 ----
out.addProperty (type, prop);
}
+ cloneToRealTranscriptHash.put(out,in);
+ realToCloneTranscriptHash.put(in,out);
return out;
}
+
+ /** Returns the real model for the cloned transcript */
+ Transcript cloneToRealTranscript(Transcript clone) {
+ return (Transcript)cloneToRealTranscriptHash.get(clone);
+ }
+ Transcript realToCloneTranscript(Transcript real) {
+ return (Transcript)realToCloneTranscriptHash.get(real);
+ }
/**
Index: MouseManager.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/Attic/MouseManager.java,v
retrieving revision 1.1.2.2
retrieving revision 1.1.2.3
diff -C2 -d -r1.1.2.2 -r1.1.2.3
*** MouseManager.java 28 May 2002 02:38:06 -0000 1.1.2.2
--- MouseManager.java 30 May 2002 23:48:35 -0000 1.1.2.3
***************
*** 46,50 ****
//selectionManager.select(newPick,exclusiveSelection,selectParents);
! selectionManager.select(clickedFeatures,exclusiveSelection,selectParents);
}
--- 46,51 ----
//selectionManager.select(newPick,exclusiveSelection,selectParents);
! selectionManager.select(clickedFeatures,exclusiveSelection,selectParents,
! apolloPanel);
}
Index: Selection.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/Selection.java,v
retrieving revision 1.16.2.6
retrieving revision 1.16.2.7
diff -C2 -d -r1.16.2.6 -r1.16.2.7
*** Selection.java 29 May 2002 23:19:15 -0000 1.16.2.6
--- Selection.java 30 May 2002 23:48:35 -0000 1.16.2.7
***************
*** 116,121 ****
/** This method takes opposite approach from above method. Selection only has model.
* views have view features. Views get queried to see which model items their
! * view features contains. This means we dont have to keep view features in selection.
! * nor view sources. just model.
*/
private Vector getSelected(ViewI vw) {
--- 116,121 ----
/** This method takes opposite approach from above method. Selection only has model.
* views have view features. Views get queried to see which model items their
! * view features contains. This means we dont have to keep view features in
! * selection, nor view sources, just model.
*/
private Vector getSelected(ViewI vw) {
Index: SelectionManager.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/Attic/SelectionManager.java,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** SelectionManager.java 29 May 2002 23:19:15 -0000 1.1.2.4
--- SelectionManager.java 30 May 2002 23:48:35 -0000 1.1.2.5
***************
*** 3,6 ****
--- 3,7 ----
import apollo.datamodel.FeatureList;
import apollo.datamodel.SeqFeatureI;
+ import apollo.gui.event.FeatureSelectionEvent;
/**
***************
*** 21,24 ****
--- 22,26 ----
private ApolloPanel apolloPanel;
+ private Controller controller; // for now
SelectionManager() {}
***************
*** 29,33 ****
/** Process selection of Selection */
//void select(Selection sel,boolean exclusiveSelection,boolean selectParents) {
! void select(FeatureList feats,boolean exclusiveSelection,boolean selectParents) {
if (exclusiveSelection) clearSelections();
//if (selectParents) apolloPanel.getPickViewFocus().selectParents(sel);
--- 31,36 ----
/** Process selection of Selection */
//void select(Selection sel,boolean exclusiveSelection,boolean selectParents) {
! void select(FeatureList feats,boolean exclusiveSelection,boolean selectParents,
! Object source) {
if (exclusiveSelection) clearSelections();
//if (selectParents) apolloPanel.getPickViewFocus().selectParents(sel);
***************
*** 40,52 ****
// eventually wont be necasary
// replace with selectionListener.select(selectionEvent)
! apolloPanel.fireFeatureSelectionEvent(newPick);
//apolloPanel.highlightEdges(sel,true);
//apolloPanel.repaint();
}
! void select(SeqFeatureI feat) {
FeatureList fl = new FeatureList();
fl.addFeature(feat);
! select(fl,true,false);
}
--- 43,56 ----
// eventually wont be necasary
// replace with selectionListener.select(selectionEvent)
! //apolloPanel.fireFeatureSelectionEvent(newPick);
! fireFeatureSelectionEvent(newPick,source);
//apolloPanel.highlightEdges(sel,true);
//apolloPanel.repaint();
}
! void select(SeqFeatureI feat,Object source) {
FeatureList fl = new FeatureList();
fl.addFeature(feat);
! select(fl,true,false,source);
}
***************
*** 62,65 ****
--- 66,77 ----
siteViews[i].clearSelections();
}
+ }
+
+ // for now - eventually wont need - incremental change
+ void setController(Controller c) { controller = c; }
+
+ private void fireFeatureSelectionEvent(Selection sel,Object source) {
+ FeatureSelectionEvent e = new FeatureSelectionEvent(source,sel);
+ controller.handleFeatureSelectionEvent(e);
}
}
Index: TablePanel.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/TablePanel.java,v
retrieving revision 1.4.2.7
retrieving revision 1.4.2.8
diff -C2 -d -r1.4.2.7 -r1.4.2.8
*** TablePanel.java 29 May 2002 23:19:15 -0000 1.4.2.7
--- TablePanel.java 30 May 2002 23:48:35 -0000 1.4.2.8
***************
*** 155,159 ****
// = new FeatureSelectionEvent(this, selected);
//controller.handleFeatureSelectionEvent(evt);
! selectionManager.select(feature);
setToFeature (feature);
}
--- 155,159 ----
// = new FeatureSelectionEvent(this, selected);
//controller.handleFeatureSelectionEvent(evt);
! selectionManager.select(feature,this);
setToFeature (feature);
}
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