/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
import java.awt.event.*;\r
import java.util.*;\r
\r
-\r
-public class AlignFrame extends GAlignFrame\r
+public class AlignFrame\r
+ extends GAlignFrame\r
{\r
final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
+ final AlignViewport viewport;\r
public static final int NEW_WINDOW_WIDTH = 700;\r
public static final int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
try\r
{\r
treeFile = treeFile;\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
+ getCodeBase() + treeFile, "URL");\r
fin.parse();\r
\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
+ fin, "FromFile", applet.getCodeBase() + treeFile);\r
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
addTreeMenuItem(tp, treeFile);\r
}\r
}\r
}\r
\r
-\r
}\r
\r
public void inputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
}\r
\r
-\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);\r
- cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\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
+ viewport.getAlignment().\r
+ getSequences()));\r
}\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
Stack redoList = new Stack();\r
\r
void updateEditMenuBar()\r
- {\r
- if(historyList.size()>0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem)historyList.peek();\r
- undoMenuItem.setLabel("Undo "+hi.getDescription());\r
- }\r
- else\r
- {\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- }\r
+ {\r
+ if (historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ HistoryItem hi = (HistoryItem) historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ }\r
\r
- if(redoList.size()>0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem)redoList.peek();\r
- redoMenuItem.setLabel("Redo "+hi.getDescription());\r
- }\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- }\r
- }\r
-\r
- public void addHistoryItem(HistoryItem hi)\r
- {\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem)historyList.pop();\r
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));\r
- restoreHistoryItem(hi);\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem)redoList.pop();\r
- restoreHistoryItem(hi);\r
- updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
- }\r
+ if (redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+ HistoryItem hi = (HistoryItem) redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ }\r
+ }\r
+\r
+ public void addHistoryItem(HistoryItem hi)\r
+ {\r
+ historyList.push(hi);\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
+ HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ }\r
\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) redoList.pop();\r
+ restoreHistoryItem(hi);\r
+ updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ alignPanel.repaint();\r
+ }\r
\r
- // used by undo and redo\r
- void restoreHistoryItem(HistoryItem hi)\r
- {\r
- if(hi.getType()== HistoryItem.SORT)\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
+ {\r
+ if (hi.getType() == HistoryItem.SORT)\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
{\r
- for(int i=0; i<hi.getSequences().size(); i++)\r
- viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);\r
+ viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
+ elementAt(i), i);\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
{\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
+ if (restore.getLength() == 0)\r
{\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
- if(restore.getLength()==0)\r
- {\r
- // log.System.out.println(hi.getHidden().elementAt(i));\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(\r
- restore,\r
- hi.getAlignIndex(i));\r
- }\r
- else\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ // log.System.out.println(hi.getHidden().elementAt(i));\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ viewport.alignment.getSequences().insertElementAt(\r
+ restore,\r
+ hi.getAlignIndex(i));\r
}\r
- if(hi.getType()==HistoryItem.PASTE)\r
+ else\r
{\r
- for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)\r
- viewport.alignment.deleteSequence(i);\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
}\r
}\r
+ if (hi.getType() == HistoryItem.PASTE)\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 1;\r
+ i > hi.getSequences().size() - 1; i--)\r
+ {\r
+ viewport.alignment.deleteSequence(i);\r
+ }\r
+ }\r
+ }\r
\r
- updateEditMenuBar();\r
-\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
- }\r
+ updateEditMenuBar();\r
\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
+ }\r
\r
public void moveSelectedSequences(boolean up)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
if (sg == null)\r
+ {\r
return;\r
+ }\r
\r
if (up)\r
{\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
if (!sg.sequences.contains(seq))\r
+ {\r
continue;\r
+ }\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
if (sg.sequences.contains(temp))\r
+ {\r
continue;\r
+ }\r
\r
viewport.alignment.getSequences().setElementAt(temp, i);\r
viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
if (!sg.sequences.contains(seq))\r
+ {\r
continue;\r
+ }\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
if (sg.sequences.contains(temp))\r
+ {\r
continue;\r
+ }\r
\r
viewport.alignment.getSequences().setElementAt(temp, i);\r
viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
alignPanel.repaint();\r
}\r
\r
-\r
StringBuffer copiedSequences;\r
protected void copy_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getSelectionGroup()==null)\r
- return;\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- copiedSequences = new StringBuffer();\r
- Hashtable orderedSeqs = new Hashtable();\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ copiedSequences = new StringBuffer();\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index+"", seq);\r
- }\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
\r
- int index=0;\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
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
- break;\r
- }\r
- else\r
- index++;\r
- }\r
+ int index = 0;\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
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
\r
- copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
- +seq.findPosition( sg.getEndRes() )+ "\t"\r
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\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
+ }\r
\r
}\r
\r
-\r
protected void pasteNew_actionPerformed(ActionEvent e)\r
{\r
paste(true);\r
\r
protected void pasteThis_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
+ HistoryItem.PASTE));\r
paste(false);\r
}\r
\r
void paste(boolean newAlignment)\r
{\r
- try{\r
+ try\r
+ {\r
if (copiedSequences == null)\r
+ {\r
return;\r
+ }\r
\r
StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
Vector seqs = new Vector();\r
String name = st.nextToken();\r
int start = Integer.parseInt(st.nextToken());\r
int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
+ Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
\r
- if(!newAlignment)\r
+ if (!newAlignment)\r
+ {\r
viewport.alignment.addSequence(sequence);\r
+ }\r
else\r
+ {\r
seqs.addElement(sequence);\r
+ }\r
}\r
\r
- if(newAlignment)\r
+ if (newAlignment)\r
{\r
SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- for(int i=0; i<seqs.size(); i++)\r
- newSeqs[i] = (SequenceI)seqs.elementAt(i);\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
String newtitle = new String("Copied sequences");\r
- if( getTitle().startsWith("Copied sequences"))\r
- newtitle = getTitle();\r
- else\r
- newtitle = newtitle.concat("- from "+getTitle());\r
- jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
+ if (getTitle().startsWith("Copied sequences"))\r
+ {\r
+ newtitle = getTitle();\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + getTitle());\r
+ }\r
+ jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
}\r
else\r
{\r
alignPanel.repaint();\r
}\r
\r
- }catch(Exception ex){}// could be anything being pasted in here\r
+ }\r
+ catch (Exception ex)\r
+ {} // could be anything being pasted in here\r
\r
}\r
\r
-\r
protected void cut_actionPerformed(ActionEvent e)\r
{\r
copy_actionPerformed(null);\r
\r
protected void delete_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\r
if (viewport.getSelectionGroup() == null)\r
+ {\r
return;\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\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
+ SequenceGroup sg = viewport.getSelectionGroup();\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(seq.getSequence().length()<1)\r
- viewport.getAlignment().deleteSequence(seq);\r
+ if (seq.getSequence().length() < 1)\r
+ {\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ }\r
else\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
+ {\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
+ }\r
\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getSize().height);\r
- if(viewport.getAlignment().getHeight()<1)\r
- try\r
- {\r
- this.setVisible(false);\r
- }catch(Exception ex){}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
+ viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setVisible(false);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
\r
}\r
\r
-\r
-\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\r
alignPanel.repaint();\r
}\r
\r
-\r
-\r
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = new SequenceGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
sg.setEndRes(viewport.alignment.getWidth());\r
viewport.setSelectionGroup(sg);\r
alignPanel.repaint();\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));\r
+ }\r
\r
PaintRefresher.Refresh(null);\r
}\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
- addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,\r
+ addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
HistoryItem.HIDE));\r
int min = colSel.getMin();\r
viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0,min);\r
+ colSel.compensateForEdit(0, min);\r
\r
- if(viewport.getSelectionGroup()!=null)\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(!sg.adjustForRemoveLeft(min))\r
+ if (!sg.adjustForRemoveLeft(min))\r
+ {\r
viewport.alignment.deleteGroup(sg);\r
+ }\r
}\r
\r
alignPanel.repaint();\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
- addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,\r
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
HistoryItem.HIDE));\r
int max = colSel.getMax();\r
viewport.getAlignment().trimRight(max);\r
- if(viewport.getSelectionGroup()!=null)\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(!sg.adjustForRemoveRight(max))\r
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
viewport.alignment.deleteGroup(sg);\r
+ }\r
}\r
\r
-\r
-\r
alignPanel.repaint();\r
}\r
\r
HistoryItem.HIDE));\r
SequenceI current;\r
int jSize;\r
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
current = viewport.getAlignment().getSequenceAt(i);\r
jSize = current.getLength();\r
- for (int j=0; j < jSize; j++)\r
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+ for (int j = 0; j < jSize; j++)\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
current.deleteCharAt(j);\r
j--;\r
jSize--;\r
}\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
\r
-\r
public void font_actionPerformed(ActionEvent e)\r
{\r
Frame frame = new Frame();\r
- FontChooser fc = new FontChooser( alignPanel, frame);\r
+ FontChooser fc = new FontChooser(alignPanel, frame);\r
frame.add(fc);\r
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
\r
}\r
\r
protected void fullSeqId_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowFullId( fullSeqId.getState() );\r
+ viewport.setShowFullId(fullSeqId.getState());\r
alignPanel.fontChanged();\r
alignPanel.repaint();\r
}\r
\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setColourText( colourTextMenuItem.getState() );\r
- alignPanel.repaint();\r
+ viewport.setColourText(colourTextMenuItem.getState());\r
+ alignPanel.repaint();\r
}\r
\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setWrapAlignment( wrapMenuItem.getState() );\r
- alignPanel.setWrapAlignment( wrapMenuItem.getState() );\r
- scaleAbove.setEnabled( wrapMenuItem.getState() );\r
- scaleLeft.setEnabled( wrapMenuItem.getState());\r
- scaleRight.setEnabled( wrapMenuItem.getState());\r
+ viewport.setWrapAlignment(wrapMenuItem.getState());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
+ scaleAbove.setEnabled(wrapMenuItem.getState());\r
+ scaleLeft.setEnabled(wrapMenuItem.getState());\r
+ scaleRight.setEnabled(wrapMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
alignPanel.repaint();\r
}\r
\r
-\r
-\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowBoxes( viewBoxesMenuItem.getState() );\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowText( viewTextMenuItem.getState() );\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
-\r
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setRenderGaps(renderGapsMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
-\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\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
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
}\r
\r
public void overviewMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if (alignPanel.overviewPanel != null)\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
return;\r
+ }\r
\r
Frame frame = new Frame();\r
OverviewPanel overview = new OverviewPanel(alignPanel);\r
frame.add(overview);\r
// +50 must allow for applet frame window\r
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.preferredSize().width, overview.preferredSize().height+50);\r
+ overview.preferredSize().width,\r
+ overview.preferredSize().height + 50);\r
\r
frame.pack();\r
frame.addWindowListener(new WindowAdapter()\r
- { public void windowClosing(WindowEvent e)\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
{\r
- alignPanel.setOverviewPanel(null);\r
+ alignPanel.setOverviewPanel(null);\r
};\r
});\r
\r
- alignPanel.setOverviewPanel( overview );\r
-\r
+ alignPanel.setOverviewPanel(overview);\r
\r
}\r
\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- changeColour( null );\r
+ changeColour(null);\r
}\r
\r
-\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
}\r
\r
public void zappoColour_actionPerformed(ActionEvent e)\r
changeColour(new TaylorColourScheme());\r
}\r
\r
-\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour( new HydrophobicColourScheme() );\r
+ changeColour(new HydrophobicColourScheme());\r
}\r
\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new HelixColourScheme() );\r
+ changeColour(new HelixColourScheme());\r
}\r
\r
-\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new StrandColourScheme());\r
}\r
\r
-\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new TurnColourScheme());\r
}\r
\r
-\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new BuriedColourScheme() );\r
+ changeColour(new BuriedColourScheme());\r
}\r
\r
public void nucleotideColour_actionPerformed(ActionEvent e)\r
changeColour(new NucleotideColourScheme());\r
}\r
\r
-\r
protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
}\r
\r
-\r
-\r
void changeColour(ColourSchemeI cs)\r
{\r
int threshold = 0;\r
\r
- if ( viewport.getAbovePIDThreshold() )\r
+ if (viewport.getAbovePIDThreshold())\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
\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
+ {\r
( (ScoreColourScheme) cs).setThreshold(0);\r
-\r
-\r
+ }\r
\r
if (viewport.getConservationSelected())\r
{\r
ccs = new ConservationColourScheme(c, cs);\r
\r
// MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( viewport.vconsensus );\r
+ ccs.setConsensus(viewport.vconsensus);\r
viewport.setGlobalColourScheme(ccs);\r
\r
SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
}\r
else\r
{\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- cs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(cs);\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ if (cs != null)\r
+ {\r
+ cs.setConsensus(viewport.vconsensus);\r
+ }\r
+ viewport.setGlobalColourScheme(cs);\r
}\r
\r
-\r
- if(viewport.getColourAppliesToAllGroups())\r
+ if (viewport.getColourAppliesToAllGroups())\r
{\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
}\r
else\r
+ {\r
try\r
{\r
sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
ex.printStackTrace();\r
sg.cs = cs;\r
}\r
+ }\r
\r
- if(viewport.getAbovePIDThreshold())\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
\r
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
}\r
\r
- if( viewport.getConservationSelected() )\r
+ if (viewport.getConservationSelected())\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0, viewport.alignment.getWidth()-1);\r
+ sg.sequences, 0,\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
+ ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
sg.cs = ccs;\r
}\r
else\r
}\r
}\r
\r
- if(alignPanel.getOverviewPanel()!=null)\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
\r
alignPanel.repaint();\r
}\r
\r
protected void modifyPID_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
+ "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
}\r
\r
protected void modifyConservation_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getConservationSelected())\r
+ if (viewport.getConservationSelected())\r
{\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
"Background");\r
}\r
}\r
\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setConservationSelected(conservationMenuItem.getState());\r
\r
viewport.setAbovePIDThreshold(false);\r
abovePIDThreshold.setState(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
+ }\r
else\r
- changeColour( cs );\r
+ {\r
+ changeColour(cs);\r
+ }\r
\r
modifyConservation_actionPerformed(null);\r
}\r
\r
ColourSchemeI cs = viewport.getGlobalColourScheme();\r
\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
+ }\r
else\r
- changeColour( cs );\r
+ {\r
+ changeColour(cs);\r
+ }\r
\r
modifyPID_actionPerformed(null);\r
}\r
\r
-\r
-\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
+ UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
}\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour( new PIDColourScheme() );\r
+ changeColour(new PIDColourScheme());\r
}\r
\r
-\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new Blosum62ColourScheme() );\r
+ changeColour(new Blosum62ColourScheme());\r
}\r
\r
-\r
-\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));\r
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(),\r
+ viewport.getAlignment().getSequenceAt(0));\r
alignPanel.repaint();\r
}\r
\r
public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));\r
- AlignmentSorter.sortByID( viewport.getAlignment() );\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
alignPanel.repaint();\r
}\r
\r
public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));\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
RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
Frame frame = new Frame();\r
frame.add(sp);\r
- jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
+ 400, 120);\r
\r
}\r
\r
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getSelectionGroup().getSize()>1)\r
+ if (viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(viewport));\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
\r
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
- || viewport.getAlignment().getHeight()<4)\r
+ if ( (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize() < 4 &&\r
+ viewport.getSelectionGroup().getSize() > 0)\r
+ || viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
}\r
\r
- try{\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", 400, 400);\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- }\r
-\r
+ jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
+ 400, 400);\r
+ }\r
+ catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ }\r
\r
}\r
\r
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
}\r
\r
-\r
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
//are the sequences aligned?\r
- if(!viewport.alignment.isAligned())\r
+ if (!viewport.alignment.isAligned())\r
{\r
return;\r
}\r
type, pwType, 0, viewport.alignment.getWidth());\r
}\r
\r
- addTreeMenuItem(tp, title);\r
+ addTreeMenuItem(tp, title);\r
\r
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
\r
void addTreeMenuItem(final TreePanel treePanel, String title)\r
});\r
}\r
\r
- protected void documentation_actionPerformed(ActionEvent e) {\r
+ protected void documentation_actionPerformed(ActionEvent e)\r
+ {\r
\r
jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
\r
\r
protected void about_actionPerformed(ActionEvent e)\r
{\r
- class AboutPanel extends Canvas\r
+ class AboutPanel\r
+ extends Canvas\r
{\r
public void paint(Graphics g)\r
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,getSize().width, getSize().height);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
FontMetrics fm = g.getFontMetrics();\r
int fh = fm.getHeight();\r
- int y=5, x=7;\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 2.0", 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.",x,y+=fh*2);\r
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);\r
- g.drawString("For any issues relating to Jalview, email help@jalview.org", x,y+=fh);\r
- g.drawString("If you use JalView, please cite:",x,y+=fh+8);\r
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);\r
- g.drawString("Bioinformatics, 2004 12;426-7.",x,y+=fh);\r
+ g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
+ x, y += fh * 2);\r
+ g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "For any issues relating to Jalview, email help@jalview.org", x,\r
+ y += fh);\r
+ g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
+ g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
+ x, y += fh);\r
+ g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);\r
}\r
}\r
+\r
Frame frame = new Frame();\r
frame.add(new AboutPanel());\r
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);\r
-\r
-\r
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff