public static final int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
\r
- public AlignFrame(AlignmentI al)\r
- {\r
- this.applet = null;\r
- viewport = new AlignViewport(al, null);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- add(alignPanel);\r
- alignPanel.validate();\r
-\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- closeMenuItem_actionPerformed(null);\r
- }\r
- });\r
-\r
- }\r
-\r
\r
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
{\r
}\r
}\r
\r
+ String param = applet.getParameter("sortBy");\r
+ if(param!=null)\r
+ {\r
+ if (param.equalsIgnoreCase("Id"))\r
+ sortIDMenuItem_actionPerformed(null);\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
+ }\r
+\r
this.addWindowListener(new WindowAdapter()\r
{\r
public void windowClosing(WindowEvent e)\r
}\r
});\r
\r
-\r
-\r
+ viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(java.beans.PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ alignmentChanged();\r
+ }\r
+ }\r
+ });\r
}\r
\r
public void inputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame,\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\r
- resetAllColourSchemes();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
HistoryItem hi = (HistoryItem) redoList.pop();\r
restoreHistoryItem(hi);\r
updateEditMenuBar();\r
- viewport.updateConsensus();\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
// used by undo and redo\r
\r
updateEditMenuBar();\r
\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
public void moveSelectedSequences(boolean up)\r
{\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
}\r
catch (Exception ex)\r
{}\r
}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\r
}\r
\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
}\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
}\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
- viewport.updateConservation();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ public void alignmentChanged()\r
+ {\r
viewport.updateConsensus();\r
+ viewport.updateConservation ();\r
resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
ColourSchemeI cs = viewport.globalColourScheme;\r
if(cs!=null)\r
{\r
- cs.setConsensus(viewport.vconsensus);\r
- if(cs.conservationApplied())\r
- {\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\r
+ }\r
\r
- cs.setConservation(c);\r
- }\r
- }\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
\r
- if(viewport.getGlobalColourScheme()!=null\r
- && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
+ cs.setConservation(c);\r
+ }\r
}\r
\r
int s, sSize = viewport.alignment.getGroups().size();\r
{\r
((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
}\r
-\r
sg.recalcConservation();\r
-\r
}\r
}\r
\r
if (viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
- frame.add(new PairwiseAlignPanel(viewport));\r
+ frame.add(new PairwiseAlignPanel(alignPanel));\r
jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
}\r
}\r