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
}\r
\r
+\r
}\r
\r
public void inputText_actionPerformed(ActionEvent e)\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
+ if(endRes>0)\r
+ {\r
+ endRes += seq.getStart() -1;\r
}\r
- }\r
\r
- copiedSequences.append(seq.getName() + "\t" +\r
- seq.findPosition(sg.getStartRes()) + "\t"\r
- + seq.findPosition(sg.getEndRes()) + "\t"\r
- +\r
- sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\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
return;\r
}\r
\r
+\r
SequenceGroup sg = viewport.getSelectionGroup();\r
+ boolean allSequences = false;\r
+ if(sg.sequences.size()==viewport.alignment.getHeight())\r
+ allSequences = true;\r
+\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (allSequences)\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+\r
if (seq.getSequence().length() < 1)\r
{\r
viewport.getAlignment().deleteSequence(seq);\r
SequenceGroup sg = new SequenceGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
- sg.addSequence(viewport.getAlignment().getSequenceAt(i));\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
sg.setEndRes(viewport.alignment.getWidth());\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
+ PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
SequenceGroup sg = viewport.getSelectionGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));\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
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Remove Gaps",\r
- viewport.alignment,\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
+\r
SequenceI current;\r
int jSize;\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+\r
+ Vector seqs=null;\r
+\r
+ int start=0, end = viewport.alignment.getWidth();\r
+\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().sequences != null\r
+ && viewport.getSelectionGroup().sequences.size()>0)\r
+ {\r
+ seqs = viewport.getSelectionGroup().sequences;\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ seqs = viewport.alignment.getSequences();\r
+\r
+ for (int i = 0; i <seqs.size(); i++)\r
{\r
- current = viewport.getAlignment().getSequenceAt(i);\r
+ current = (SequenceI)seqs.elementAt(i);\r
jSize = current.getLength();\r
- for (int j = 0; j < jSize; j++)\r
+\r
+ int j = start;\r
+ do\r
{\r
if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
j--;\r
jSize--;\r
}\r
+ j++;\r
}\r
+ while(j < end && j < jSize) ;\r
}\r
+\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
alignPanel.repaint();\r
}\r
\r
+\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
Finder finder = new Finder(alignPanel);\r
{\r
threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
- }\r
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
\r
viewport.setGlobalColourScheme(cs);\r
}\r
- else if (cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
+ else\r
{\r
- ( (ScoreColourScheme) cs).setThreshold(0);\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
}\r
\r
if (viewport.getConservationSelected())\r
{\r
- ConservationColourScheme ccs = null;\r
\r
Alignment al = (Alignment) viewport.alignment;\r
Conservation c = new Conservation("All",\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
\r
- ccs = new ConservationColourScheme(c, cs);\r
+ cs.setConservation(c);\r
\r
// MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(ccs);\r
+ cs.setConsensus(viewport.vconsensus);\r
+ viewport.setGlobalColourScheme(cs);\r
\r
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
+ SliderPanel.setConservationSlider(alignPanel, cs, "Background");\r
\r
}\r
else\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
+ if(cs==null)\r
+ {\r
+ sg.cs = null;\r
+ continue;\r
+ }\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
+ cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
+ sg.cs = cxs;\r
}\r
else\r
{\r
\r
if (viewport.getAbovePIDThreshold())\r
{\r
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\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
+ cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ sg.cs = cs;\r
}\r
else\r
{\r
}\r
}\r
\r
+ updateCSConsensus();\r
+\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
alignPanel.getOverviewPanel().updateOverviewImage();\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
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
addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
HistoryItem.SORT));\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
alignPanel.repaint();\r
+\r
}\r
\r
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\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 documentation_actionPerformed(ActionEvent e)\r
{\r
-\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
-\r
+ jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
}\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 2.0", 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