import java.awt.*;\r
import java.awt.event.*;\r
import java.util.*;\r
+import java.io.InputStreamReader;\r
+import java.io.BufferedReader;\r
\r
public class AlignFrame\r
extends GAlignFrame\r
{\r
final AlignmentPanel alignPanel;\r
final AlignViewport viewport;\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
+ public static int NEW_WINDOW_WIDTH = 700;\r
+ public static 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
\r
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
{\r
add(alignPanel);\r
alignPanel.validate();\r
\r
- String treeFile = applet.getParameter("treeFile");\r
- TreePanel treepanel = null;\r
- if (treeFile != null)\r
+ if(applet!=null)\r
{\r
- try\r
+ String treeFile = applet.getParameter("treeFile");\r
+ if (treeFile != null)\r
{\r
- treeFile = treeFile;\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
- getCodeBase() + treeFile, "URL");\r
- fin.parse();\r
+ try\r
+ {\r
+ treeFile = treeFile;\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
+ getCodeBase() + treeFile, "URL");\r
+ fin.parse();\r
\r
- if (fin.getTree() != null)\r
+ if (fin.getTree() != null)\r
+ {\r
+ TreePanel tp = null;\r
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+ fin, "FromFile", applet.getCodeBase() + treeFile);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
{\r
- TreePanel tp = null;\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase() + treeFile);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
+ ex.printStackTrace();\r
}\r
}\r
- catch (Exception ex)\r
+\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != null)\r
{\r
- ex.printStackTrace();\r
+ if (param.equalsIgnoreCase("Id"))\r
+ sortIDMenuItem_actionPerformed(null);\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
+ }\r
+\r
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
+ {\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
}\r
}\r
\r
+ this.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ closeMenuItem_actionPerformed(null);\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
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
- cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
viewport.getAlignment().\r
getSequences()));\r
}\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ PaintRefresher.components.remove(viewport.alignment);\r
dispose();\r
+ if(PaintRefresher.components.size()==0 && applet==null)\r
+ System.exit(0);\r
}\r
\r
Stack historyList = new Stack();\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\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
- 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
orderedSeqs.put(index + "", seq);\r
}\r
\r
- int index = 0;\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
- SequenceI seq = null;\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
{\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
- break;\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
}\r
- else\r
+\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
+\r
+ for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
{\r
- index++;\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
}\r
- }\r
\r
- copiedSequences.append(seq.getName() + "\t" +\r
- seq.findPosition(sg.getStartRes()) + "\t"\r
- + seq.findPosition(sg.getEndRes()) + "\t"\r
- +\r
- seq.getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ if(endRes>0)\r
+ {\r
+ endRes += seq.getStart() -1;\r
+ }\r
+\r
+ copiedSequences.append(seq.getName() + "\t" +\r
+ startRes + "\t" +\r
+ endRes + "\t" +\r
+ seq.getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
}\r
\r
}\r
{\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\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
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\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);\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
- PaintRefresher.Refresh(null);\r
+ alignPanel.repaint();\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
\r
- PaintRefresher.Refresh(null);\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\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
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\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
{\r
seqs = viewport.getSelectionGroup().sequences;\r
start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes();\r
+ end = viewport.getSelectionGroup().getEndRes()+1;\r
}\r
else\r
seqs = viewport.alignment.getSequences();\r
\r
- for (int i = 0; i <seqs.size(); i++)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- current = (SequenceI)seqs.elementAt(i);\r
+ current = (SequenceI) seqs.elementAt(i);\r
jSize = current.getLength();\r
\r
+ // Removing a range is much quicker than removing gaps\r
+ // one by one for long sequences\r
int j = start;\r
+ int rangeStart=-1, rangeEnd=-1;\r
+\r
do\r
{\r
if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
+ if(rangeStart==-1)\r
+ {\r
+ rangeStart = j;\r
+ rangeEnd = j+1;\r
+ }\r
+ else\r
+ {\r
+ rangeEnd++;\r
+ }\r
+ j++;\r
}\r
- j++;\r
+ else\r
+ {\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ j-=rangeEnd-rangeStart;\r
+ jSize-=rangeEnd-rangeStart;\r
+ rangeStart = -1;\r
+ rangeEnd = -1;\r
+ }\r
+ else\r
+ j++;\r
+ }\r
+ }\r
+ while (j < end && j < jSize);\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
}\r
- while(j < end && j < jSize) ;\r
}\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
\r
- viewport.updateConservation();\r
+ public void alignmentChanged()\r
+ {\r
viewport.updateConsensus();\r
+ viewport.updateConservation ();\r
+ resetAllColourSchemes();\r
+ if(alignPanel.overviewPanel!=null)\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
alignPanel.repaint();\r
}\r
\r
+ void resetAllColourSchemes()\r
+ {\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\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
+ cs.setConservation(c);\r
+ }\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
+ sg.recalcConservation();\r
+ }\r
+ }\r
+\r
+\r
\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
public void font_actionPerformed(ActionEvent e)\r
{\r
- Frame frame = new Frame();\r
- FontChooser fc = new FontChooser(alignPanel, frame);\r
- frame.add(fc);\r
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
-\r
+ new FontChooser(alignPanel);\r
}\r
\r
protected void fullSeqId_actionPerformed(ActionEvent e)\r
\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setState(false);\r
- return;\r
- }\r
viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\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
- if (cs instanceof ResidueColourScheme)\r
+ if (viewport.getAbovePIDThreshold())\r
{\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
- }\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else if (cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
- }\r
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
\r
- if (viewport.getConservationSelected())\r
- {\r
- ConservationColourScheme ccs = null;\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
- ccs = new ConservationColourScheme(c, cs);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(ccs);\r
+ cs.setConservation(c);\r
\r
- SliderPanel.setConservationSlider(alignPanel, ccs, "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
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
-\r
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\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
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- sg.cs = ccs;\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
+\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
alignPanel.repaint();\r
}\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
viewport.setAbovePIDThreshold(false);\r
abovePIDThreshold.setState(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- changeColour( ( (ConservationColourScheme) cs).cs);\r
- }\r
- else\r
- {\r
- changeColour(cs);\r
- }\r
+ changeColour(viewport.getGlobalColourScheme());\r
\r
modifyConservation_actionPerformed(null);\r
}\r
conservationMenuItem.setState(false);\r
viewport.setConservationSelected(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- changeColour( ( (ConservationColourScheme) cs).cs);\r
- }\r
- else\r
- {\r
- changeColour(cs);\r
- }\r
+ changeColour(viewport.getGlobalColourScheme());\r
\r
modifyPID_actionPerformed(null);\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
\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.repaint();\r
+ }\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
viewport.getSelectionGroup().getSize() < 4 &&\r
\r
try\r
{\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- Frame frame = new Frame();\r
- frame.add(pcaPanel);\r
- jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
- 400, 400);\r
+ new PCAPanel(viewport);\r
}\r
catch (java.lang.OutOfMemoryError ex)\r
{\r
//are the sequences aligned?\r
if (!viewport.alignment.isAligned())\r
{\r
- return;\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.repaint();\r
+\r
}\r
\r
final TreePanel tp;\r
\r
protected void about_actionPerformed(ActionEvent e)\r
{\r
- class AboutPanel\r
- extends Canvas\r
+\r
+ class AboutPanel extends Canvas\r
{\r
+ String version;\r
+ public AboutPanel(String version)\r
+ { this.version = version; }\r
+\r
public void paint(Graphics g)\r
{\r
g.setColor(Color.white);\r
int y = 5, x = 7;\r
g.setColor(Color.black);\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("JalView - Release 2.01", 200, y += fh);\r
+ g.drawString("Jalview - Release "+version, 200, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
x, y += fh * 2);\r
}\r
}\r
\r
+ String version = "test";\r
+ java.net.URL url = getClass().getResource("/.build_properties");\r
+ if (url != null)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader reader = new BufferedReader(new InputStreamReader(\r
+ url.openStream()));\r
+ String line;\r
+ while ( (line = reader.readLine()) != null)\r
+ {\r
+ if (line.indexOf("VERSION") > -1)\r
+ {\r
+ version = line.substring(line.indexOf("=") + 1);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+\r
Frame frame = new Frame();\r
- frame.add(new AboutPanel());\r
+ frame.add(new AboutPanel(version));\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff