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
this.applet = applet;\r
alignPanel.validate();\r
\r
String treeFile = applet.getParameter("treeFile");\r
- TreePanel treepanel = null;\r
if (treeFile != null)\r
{\r
try\r
}\r
}\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
\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ PaintRefresher.components.remove(viewport.alignment);\r
dispose();\r
}\r
\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\r
+ resetAllColourSchemes();\r
}\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
restoreHistoryItem(hi);\r
updateEditMenuBar();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
alignPanel.repaint();\r
}\r
viewport.alignment.getWidth();\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
}\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
\r
}\r
{\r
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
- sg.setEndRes(viewport.alignment.getWidth());\r
+ sg.setEndRes(viewport.alignment.getWidth()-1);\r
viewport.setSelectionGroup(sg);\r
alignPanel.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
}\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
viewport.alignment,\r
HistoryItem.HIDE));\r
+\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
viewport.getAlignment().removeGaps();\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
SequenceI current;\r
int jSize;\r
\r
while(j < end && j < jSize) ;\r
}\r
\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
+ void resetAllColourSchemes()\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
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\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
+ }\r
+\r
+ int s, sSize = viewport.alignment.getGroups().size();\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ }\r
+\r
+ sg.recalcConservation();\r
+\r
+ }\r
+ }\r
+\r
+\r
\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
{\r
int threshold = 0;\r
\r
- if (viewport.getAbovePIDThreshold())\r
+ if(cs!=null)\r
{\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
-\r
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else\r
- {\r
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
\r
- if (viewport.getConservationSelected())\r
- {\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\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
+ if (viewport.getConservationSelected())\r
+ {\r
\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\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
\r
- cs.setConservation(c);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- cs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(cs);\r
+ cs.setConservation(c);\r
\r
- SliderPanel.setConservationSlider(alignPanel, cs, "Background");\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
+ "Background"));\r
\r
- }\r
- else\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
+ }\r
+ else\r
{\r
- cs.setConsensus(viewport.vconsensus);\r
+ cs.setConservation(null);\r
}\r
- viewport.setGlobalColourScheme(cs);\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+\r
}\r
+ viewport.setGlobalColourScheme(cs);\r
\r
if (viewport.getColourAppliesToAllGroups())\r
{\r
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
- cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
- sg.cs = cxs;\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
}\r
else\r
{\r
}\r
}\r
\r
- if (viewport.getAbovePIDThreshold())\r
+ if (viewport.getAbovePIDThreshold()\r
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
}\r
+ else\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
\r
if (viewport.getConservationSelected())\r
{\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- sg.cs = cs;\r
+ sg.cs.setConservation(c);\r
}\r
else\r
{\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ sg.cs.setConservation(null);\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
}\r
\r
}\r
}\r
\r
- updateCSConsensus();\r
\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
alignPanel.repaint();\r
}\r
\r
- public void updateCSConsensus()\r
- {\r
- //Colour schemes must have their consensus updated\r
\r
- }\r
\r
protected void modifyPID_actionPerformed(ActionEvent e)\r
{\r
- if (viewport.getAbovePIDThreshold())\r
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
{\r
SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
"Background");\r
\r
protected void modifyConservation_actionPerformed(ActionEvent e)\r
{\r
- if (viewport.getConservationSelected())\r
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
{\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
"Background");\r
git://source.jalview.org / jalview.git / blobdiff