* @param avp DOCUMENT ME!\r
* @param p DOCUMENT ME!\r
*/\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+ public SeqPanel(AlignViewport av, AlignmentPanel ap)\r
{\r
linkImageURL = getClass().getResource("/images/link.gif");\r
ToolTipManager.sharedInstance().registerComponent(this);\r
ToolTipManager.sharedInstance().setInitialDelay(0);\r
ToolTipManager.sharedInstance().setDismissDelay(10000);\r
- this.av = avp;\r
+ this.av = av;\r
setBackground(Color.white);\r
\r
- seqCanvas = new SeqCanvas(avp);\r
+ seqCanvas = new SeqCanvas(ap);\r
setLayout(new BorderLayout());\r
add(seqCanvas, BorderLayout.CENTER);\r
\r
- ap = p;\r
+ this.ap = ap;\r
\r
if (!av.isDataset())\r
{\r
continue;\r
}\r
\r
+ if (features[i].featureGroup != null\r
+ && seqCanvas.fr.featureGroups!=null\r
+ && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)\r
+ && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())\r
+ continue;\r
+\r
+\r
if ( (features[i].getBegin() <= res) &&\r
(features[i].getEnd() >= res))\r
{\r
}\r
\r
features = new SequenceFeature[tmp.size()];\r
- for (int i = 0; i < tmp.size(); i++)\r
- {\r
- features[i] = (SequenceFeature) tmp.elementAt(i);\r
- }\r
+ tmp.copyInto(features);\r
\r
return features;\r
}\r
\r
- Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
- {\r
- Vector allFeatures = new Vector();\r
- int index = 0;\r
- if (seq.getSequenceFeatures() != null && av.featuresDisplayed != null)\r
- {\r
- while (index < seq.getSequenceFeatures().length)\r
- {\r
- SequenceFeature sf = seq.getSequenceFeatures()[index];\r
- if (sf.getBegin() <= res &&\r
- sf.getEnd() >= res)\r
- {\r
- if (av.featuresDisplayed.containsKey(sf.getType()))\r
- {\r
- allFeatures.addElement(sf);\r
- }\r
- }\r
- index++;\r
- }\r
- }\r
- return allFeatures;\r
- }\r
\r
void endEditing()\r
{\r
}\r
\r
endEditing();\r
-\r
- ap.paintAlignment(true);\r
}\r
\r
/**\r
\r
if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
- Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),\r
+ SequenceFeature [] allFeatures = findFeaturesAtRes(sequence.getDatasetSequence(),\r
sequence.findPosition(res));\r
Vector links = new Vector();\r
- for (int i = 0; i < allFeatures.size(); i++)\r
+ for (int i = 0; i < allFeatures.length; i++)\r
{\r
- SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
- if (sf.links != null)\r
+ if (allFeatures[i].links != null)\r
{\r
- for (int j = 0; j < sf.links.size(); j++)\r
+ for (int j = 0; j < allFeatures[i].links.size(); j++)\r
{\r
- links.addElement(sf.links.elementAt(j));\r
+ links.addElement(allFeatures[i].links.elementAt(j));\r
}\r
}\r
}\r
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
stretchGroup.getName());\r
}\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ ap.paintAlignment(true);\r
}\r
+\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
\r
- PaintRefresher.Refresh(this, av.getSequenceSetId());\r
- ap.paintAlignment(true);\r
}\r
\r
/**\r