AlignmentPanel alignPanel;\r
AlignViewport viewport;\r
\r
- Vector viewports = new Vector();\r
- Vector alignPanels = new Vector();\r
-\r
/** DOCUMENT ME!! */\r
public String currentFileFormat = null;\r
Stack historyList = new Stack();\r
public AlignFrame(AlignmentI al)\r
{\r
viewport = new AlignViewport(al);\r
- viewports.add(viewport);\r
\r
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
\r
}\r
\r
alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanels.add(alignPanel);\r
\r
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
\r
return jalview.bin.Cache.getProperty("VERSION");\r
}\r
\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ }\r
+\r
\r
public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
java.io.File.separatorChar) + 1);\r
}\r
\r
- Jalview2XML.SaveAlignment(this, file, shortName);\r
+ new Jalview2XML().SaveAlignment(this, file, shortName);\r
\r
// USE Jalview2XML to save this file\r
return true;\r
String newtitle = new String("Copied sequences");\r
\r
//>>>This is a fix for the moment, until a better solution is found!!<<<\r
- FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
- fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+\r
\r
if (title.startsWith("Copied sequences"))\r
{\r
\r
//Jalview no longer allows deletion of residues.\r
//Check here whether any residues are in selection area\r
- if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
{\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
j++;\r
}while(j<=sg.getEndRes());\r
}\r
- }\r
+ }*/\r
\r
\r
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
*/\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
+ }\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
\r
public void alignmentChanged()\r
{\r
- if(viewport.vconsensus!=null)\r
+ if(viewport.padGaps)\r
+ viewport.getAlignment().padGaps();\r
+\r
+ if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)\r
{\r
viewport.updateConsensus();\r
viewport.updateConservation();\r
{\r
addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
- if (viewport.getAlignment().padGaps())\r
- alignmentChanged();\r
+\r
+ viewport.padGaps = padGapsMenuitem.isSelected();\r
+\r
+ // if (viewport.padGaps)\r
+ alignmentChanged();\r
}\r
\r
/**\r
new PCAPanel(viewport);\r
}\r
\r
+\r
+ public void autoCalculate_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
- final TreePanel tp;\r
+ TreePanel tp;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
(viewport.getSelectionGroup().getSize() > 3))\r
}\r
\r
addTreeMenuItem(tp, title);\r
- viewport.setCurrentTree(tp.getTree());\r
\r
Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
}\r
{\r
// Add any Multiple Sequence Alignment Services\r
final JMenu msawsmenu = new JMenu("Alignment");\r
+ final AlignFrame af = this;\r
for (int i = 0, j = msaws.size(); i < j; i++)\r
{\r
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- false, true, viewport.getAlignment().getDataset());\r
+ false, true, viewport.getAlignment().getDataset(), af);\r
\r
}\r
\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- true, true, viewport.getAlignment().getDataset());\r
+ true, true, viewport.getAlignment().getDataset(), af);\r
\r
}\r
\r
jalview.datamodel.AlignmentAnnotation[] annotations\r
= viewport.alignment.getAlignmentAnnotation();\r
int a, aSize;\r
- for (int i = 0; i < annotations.length; i++)\r
+ if(annotations!=null)\r
{\r
-\r
- if (annotations[i].label.equals("Quality") ||\r
- annotations[i].label.equals("Conservation") ||\r
- annotations[i].label.equals("Consensus"))\r
+ for (int i = 0; i < annotations.length; i++)\r
{\r
- continue;\r
- }\r
-\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
\r
- aSize = viewport.alignment.getWidth()/3;\r
- jalview.datamodel.Annotation [] anots =\r
- new jalview.datamodel.Annotation[aSize];\r
+ aSize = viewport.alignment.getWidth() / 3;\r
+ jalview.datamodel.Annotation[] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
\r
- for(a=0; a<viewport.alignment.getWidth(); a++)\r
- {\r
- if( annotations[i].annotations[a]==null\r
- || annotations[i].annotations[a]==null)\r
- continue;\r
+ for (a = 0; a < viewport.alignment.getWidth(); a++)\r
+ {\r
+ if (annotations[i].annotations[a] == null\r
+ || annotations[i].annotations[a] == null)\r
+ continue;\r
\r
- anots[a/3] = new Annotation(\r
- annotations[i].annotations[a].displayCharacter,\r
- annotations[i].annotations[a].description,\r
- annotations[i].annotations[a].secondaryStructure,\r
- annotations[i].annotations[a].value,\r
- annotations[i].annotations[a].colour);\r
- }\r
+ anots[a / 3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
\r
- jalview.datamodel.AlignmentAnnotation aa\r
+ jalview.datamodel.AlignmentAnnotation aa\r
= new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
- annotations[i].description, anots );\r
- al.addAnnotation(aa);\r
+ annotations[i].description, anots);\r
+ al.addAnnotation(aa);\r
+ }\r
}\r
\r
-\r
AlignFrame af = new AlignFrame(al);\r
Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
NEW_WINDOW_WIDTH,\r
}\r
\r
// This method will attempt to load a "dropped" file first by testing\r
- // whether its and Annotation file, then group file. If both are\r
+ // whether its and Annotation file, then features file. If both are\r
// false then the user may have dropped an alignment file onto this\r
// AlignFrame\r
- void loadJalviewDataFile(String file)\r
+ public void loadJalviewDataFile(String file)\r
{\r
try{\r
boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.\r
git://source.jalview.org / jalview.git / blobdiff