+/*\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.gui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
import jalview.datamodel.*;\r
import javax.swing.*;\r
+import java.util.*;\r
import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-\r
+import jalview.analysis.Conservation;\r
\r
public class SeqPanel extends JPanel\r
{\r
\r
public SeqCanvas seqCanvas;\r
- public AlignmentPanel parent;\r
+ public AlignmentPanel ap;\r
\r
- protected int startres;\r
protected int lastres;\r
- protected int endres;\r
-\r
protected int startseq;\r
- protected int padseq;\r
+ int startEdit=-1;\r
+ int endEdit=-1;\r
\r
protected AlignViewport av;\r
\r
// if character is inserted or deleted, we will need to recalculate the conservation\r
int seqEditOccurred = -1;\r
\r
+ ScrollThread scrollThread = null;\r
+ boolean mouseDragging = false;\r
+\r
+ boolean editingSeqs = false;\r
+ boolean groupEditing = false;\r
+\r
+\r
public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
this.av = avp;\r
\r
setLayout(new BorderLayout());\r
add(seqCanvas, BorderLayout.CENTER);\r
\r
- parent = p;\r
+ ap = p;\r
\r
addMouseMotionListener( new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
- { doMouseMoved(evt); }\r
+ {\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ doMouseMoved(evt); }\r
\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if( editingSeqs )\r
doMouseDragged(evt);\r
else\r
doMouseDraggedDefineMode(evt);\r
{\r
public void mouseReleased(MouseEvent evt)\r
{\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if(editingSeqs)\r
doMouseReleased(evt);\r
else\r
doMouseReleasedDefineMode(evt);\r
+\r
}\r
public void mousePressed(MouseEvent evt)\r
{\r
+ if(av.getWrapAlignment())\r
+ return;\r
if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ if(evt.isAltDown() || evt.isControlDown())\r
+ groupEditing = true;\r
+\r
+ editingSeqs = true;\r
doMousePressed(evt);\r
+ }\r
else\r
doMousePressedDefineMode(evt);\r
}\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ if (av.getWrapAlignment() || editingSeqs)\r
+ return;\r
+ doMouseExitedDefineMode(evt);\r
+\r
+ }\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if (av.getWrapAlignment() || editingSeqs)\r
+ return;\r
+ doMouseEnteredDefineMode(evt);\r
+ }\r
\r
});\r
repaint();\r
\r
public void doMouseReleased(MouseEvent evt) {\r
\r
- int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
-\r
- endres = res;\r
+ if(seqEditOccurred>-1)\r
+ editOccurred(seqEditOccurred);\r
\r
startseq = -1;\r
- startres = -1;\r
lastres = -1;\r
- if(seqEditOccurred>-1)\r
- updateConservation(seqEditOccurred);\r
-\r
seqEditOccurred = -1;\r
+ editingSeqs = false;\r
+ groupEditing = false;\r
\r
- parent.RefreshPanels();\r
- repaint();\r
-\r
+ ap.repaint();\r
}\r
\r
public void doMousePressed(MouseEvent evt) {\r
- parent.alignFrame.addHistoryItem("sequence edit");\r
+\r
+ ap.alignFrame.addHistoryItem( new HistoryItem(\r
+ "Edit Sequence",av.alignment, HistoryItem.EDIT));\r
+\r
int seq;\r
int res;\r
\r
if (seq < av.getAlignment().getHeight() &&\r
res < av.getAlignment().getSequenceAt(seq).getLength())\r
{\r
- //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
- // Find the residue's position in the sequence (res is the position\r
- // in the alignment\r
-\r
startseq = seq;\r
-\r
- if (startseq == (av.getAlignment().getHeight() - 1))\r
- padseq = 1;\r
- else\r
- padseq = 1;\r
-\r
- startres = res;\r
lastres = res;\r
-\r
}\r
else\r
{\r
startseq = -1;\r
- startres = -1;\r
lastres = -1;\r
}\r
\r
+ startEdit = lastres;\r
+ endEdit = lastres;\r
+\r
return;\r
}\r
\r
y %= chunkHeight;\r
seq = y / av.getCharHeight() + av.getStartSeq();\r
\r
- // chunkHeight = (da.getHeight() + 2)*charHeight;\r
- // startx += chunkWidth;\r
}\r
else\r
{\r
if(seq>=av.getAlignment().getHeight())\r
return;\r
\r
- Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+ if(res>sequence.getLength())\r
+ return;\r
+\r
+ Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
String aa = "";\r
if(obj!=null)\r
aa = obj.toString();\r
\r
- StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());\r
+ StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());\r
if(aa!="")\r
text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
\r
- parent.alignFrame.statusBar.setText(text.toString());\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
+ // use aa to see if the mouse pointer is on a\r
+ if( av.showSequenceFeatures)\r
+ {\r
+ Vector features = sequence.getSequenceFeatures();\r
+ Enumeration e = features.elements();\r
+ StringBuffer sbuffer = new StringBuffer();\r
+\r
+\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ if (sf.getStart() <= sequence.findPosition(res) &&\r
+ sf.getEnd() >= sequence.findPosition(res))\r
+ {\r
+ if(sbuffer.length()>0)\r
+ sbuffer.append("; ");\r
+ sbuffer.append(sf.getType() + " " + sf.getDescription());\r
+ if(sf.getStatus().length()>0)\r
+ sbuffer.append(" ("+sf.getStatus()+")");\r
+ }\r
+\r
+ }\r
+\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+ this.setToolTipText(sbuffer.toString());\r
+ }\r
+\r
\r
}\r
\r
public void doMouseDragged(MouseEvent evt) {\r
- // If we're dragging we're editing\r
\r
- int x = evt.getX();\r
-\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
+ // If we're dragging we're editing\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
if (res < 0)\r
res = 0;\r
\r
+ if (lastres == -1 || lastres == res)\r
+ return;\r
+\r
+ boolean dragRight = true;\r
+ if (res < av.getAlignment().getWidth() && res < lastres)\r
+ dragRight = false;\r
+\r
+\r
if (res != lastres)\r
{\r
- // Group editing\r
- if (evt.isAltDown() || evt.isControlDown())\r
+ // Group editing\r
+ if (groupEditing)\r
{\r
- SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
- if (sg != null)\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if(sg==null)\r
{\r
- boolean deleteAllowed = false;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
+ lastres=-1;\r
+ return;\r
+ }\r
+\r
+ // drag to right\r
+ if(dragRight)\r
+ sg.setEndRes(sg.getEndRes() + (res-lastres));\r
+\r
+ // drag to left\r
+ else\r
{\r
- /// Are we able to delete?\r
- boolean allGaps = true;\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+ boolean deleteAllowed = false;\r
+ for (int s = 0; s < sg.getSize(); s++)\r
{\r
- SequenceI s = sg.getSequenceAt(i);\r
- for (int j = lastres-1; j >= res && allGaps; j--)\r
+ SequenceI seq = sg.getSequenceAt(s);\r
+ for (int j=res; j<lastres; j++)\r
{\r
- if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))\r
- {\r
- res = j + 1;\r
- allGaps = false;\r
- }\r
- }\r
-\r
- if(!deleteAllowed && allGaps)\r
+ if(seq.getSequence().length()<=j)\r
+ continue;\r
+\r
+ if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ res=j+1;\r
+ deleteAllowed = false;\r
+ continue;\r
+ }\r
deleteAllowed = true;\r
+ }\r
}\r
- }\r
-\r
- // drag to right\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- sg.setEndRes(sg.getEndRes() + 1);\r
-\r
- // drag to left\r
- else if (deleteAllowed && res < av.getAlignment().getWidth() &&\r
- res < lastres)\r
- sg.setEndRes(sg.getEndRes() - 1);\r
\r
+ if(!deleteAllowed)\r
+ {\r
+ lastres = -1;\r
+ return;\r
+ }\r
\r
+ sg.setEndRes(sg.getEndRes() - (lastres-res));\r
+ }\r
\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
int k = av.alignment.findIndex(s);\r
\r
// drag to right\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
+ if (dragRight)\r
for (int j = lastres; j < res; j++)\r
insertChar(j, k);\r
\r
// drag to left\r
- else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)\r
+ else\r
{\r
for (int j = res; j < lastres; j++)\r
{\r
- deleteChar(j, k);\r
- startres = res;\r
+ if(s.getLength()>j)\r
+ deleteChar(res, k);\r
}\r
}\r
}\r
- }\r
}\r
else /////Editing a single sequence///////////\r
{\r
else if (res < av.getAlignment().getWidth() && res < lastres)\r
{\r
// dragging to the left\r
- for (int j = res; j < lastres; j++)\r
+ for (int j = lastres; j > res; j--)\r
{\r
- deleteChar(j, startseq);\r
- startres = res;\r
- }\r
- }\r
+ if( jalview.util.Comparison.isGap(\r
+ av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
\r
- }\r
+ deleteChar(res, startseq);\r
+ else\r
+ {\r
+\r
+ break;\r
+ }\r
+ }\r
+ }\r
\r
+ }\r
}\r
\r
+ endEdit = res;\r
lastres = res;\r
repaint();\r
}\r
\r
public void deleteChar(int j, int seq)\r
{\r
-\r
- if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+ av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+ seqEditOccurred=seq;\r
\r
av.alignment.getWidth();\r
repaint();\r
- seqEditOccurred=seq;\r
}\r
\r
\r
- void updateConservation(int i)\r
+ void editOccurred(int i)\r
{\r
- /* Alignment al = (Alignment) av.getAlignment();\r
- SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));\r
- if(sg==null || !(sg.cs instanceof ConservationColourScheme))\r
- return;\r
+ if(endEdit==startEdit)\r
+ {\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
+ av.updateConservation();\r
+ av.updateConsensus();\r
+\r
+ // Y O Y CLUSTALX\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
+ if(ccs.cs instanceof ClustalxColourScheme)\r
+ {\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ av.alignment.getSequences(), 0,\r
+ av.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;\r
+ cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
+ ccs = new ConservationColourScheme(c, cxs);\r
+ av.setGlobalColourScheme(ccs);\r
+ }\r
+ }\r
\r
- Conservation c = sg.getConservation();\r
+ if(cs instanceof ClustalxColourScheme)\r
+ {\r
+ ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
+ av.setGlobalColourScheme(cs);\r
+ }\r
\r
- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth());\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- ccs.conserve = c;*/\r
}\r
\r
//////////////////////////////////////////\r
int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
oldSeq = seq;\r
\r
- stretchGroup = av.getRubberbandGroup();\r
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
+\r
+ if(sequence==null || res>sequence.getLength())\r
+ return;\r
+\r
+ stretchGroup = av.getSelectionGroup();\r
\r
if(stretchGroup == null)\r
- stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));\r
+ {\r
+ stretchGroup = av.alignment.findGroup( sequence );\r
+ if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
+ av.setSelectionGroup(stretchGroup);\r
+ else\r
+ stretchGroup = null;\r
+ }\r
\r
- else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))\r
+ else if(!stretchGroup.sequences.contains(sequence)\r
|| stretchGroup.getStartRes()>res\r
|| stretchGroup.getEndRes()<res)\r
{\r
stretchGroup = null;\r
\r
- SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.\r
- getAlignment().\r
- getSequenceAt(seq));\r
+ SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );\r
\r
if (allGroups != null)\r
for (int i = 0; i < allGroups.length; i++)\r
allGroups[i].getEndRes() >= res)\r
{\r
stretchGroup = allGroups[i];\r
- av.setRubberbandGroup(stretchGroup);\r
+ av.setSelectionGroup(stretchGroup);\r
break;\r
}\r
}\r
SequenceGroup sg = new SequenceGroup();\r
sg.setStartRes(res);\r
sg.setEndRes(res);\r
- sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );\r
- av.setRubberbandGroup( sg );\r
+ sg.addSequence( sequence );\r
+ av.setSelectionGroup( sg );\r
stretchGroup = sg;\r
+\r
+ if(av.getConservationSelected())\r
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
+ if(av.getAbovePIDThreshold())\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
+\r
}\r
else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);\r
pop.show(this, evt.getX(), evt.getY());\r
\r
// edit the properties of existing group\r
// Edit end res position of selected group\r
changeStartRes = true;\r
\r
+ stretchGroup.getWidth();\r
\r
- seqCanvas.paintFlag = true;\r
repaint();\r
\r
-\r
}\r
\r
boolean changeEndSeq = false;\r
\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
+ mouseDragging = false;\r
+\r
+ if(stretchGroup==null)\r
+ return;\r
+\r
+ if(stretchGroup.cs instanceof ClustalxColourScheme)\r
+ {\r
+ stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
+ repaint();\r
+ }\r
+\r
+ else if(stretchGroup.cs instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
+ stretchGroup.cs = ccs;\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
+\r
+ repaint();\r
+ }\r
+ else\r
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
+\r
+\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
+ ap.idPanel.repaint();\r
}\r
\r
\r
int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
\r
+ if(stretchGroup==null)\r
+ return;\r
+\r
+ if(res>av.alignment.getWidth())\r
+ res = av.alignment.getWidth()-1;\r
+\r
\r
if(stretchGroup.getEndRes()==res)\r
// Edit end res position of selected group\r
changeEndRes = true;\r
\r
else if(stretchGroup.getStartRes()==res)\r
- // Edit end res position of selected group\r
+ // Edit start res position of selected group\r
changeStartRes = true;\r
\r
\r
stretchGroup.setStartRes( res );\r
}\r
\r
-\r
int dragDirection = 0;\r
if (y > oldSeq)\r
dragDirection = 1;\r
else if (y < oldSeq)\r
dragDirection = -1;\r
\r
- while (y != oldSeq)\r
+ while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\r
{\r
// This routine ensures we don't skip any sequences, as the\r
// selection is quite slow.\r
}\r
else\r
{\r
+ if(seq!=null)\r
stretchGroup.addSequence(seq);\r
stretchGroup.addSequence(nextSeq);\r
}\r
}\r
oldSeq = y;\r
+ mouseDragging = true;\r
+ if(scrollThread!=null)\r
+ scrollThread.setEvent(evt);\r
\r
- seqCanvas.paintFlag = true;\r
repaint();\r
}\r
\r
+ public void doMouseEnteredDefineMode(MouseEvent e)\r
+ {\r
+ if (scrollThread != null)\r
+ scrollThread.running = false;\r
+ }\r
+\r
+ public void doMouseExitedDefineMode(MouseEvent e)\r
+ {\r
+ if (av.getWrapAlignment())\r
+ return;\r
+\r
+ if(mouseDragging)\r
+ scrollThread = new ScrollThread();\r
+\r
+ }\r
+ // this class allows scrolling off the bottom of the visible alignment\r
+ class ScrollThread extends Thread\r
+ {\r
+ MouseEvent evt;\r
+ boolean running = false;\r
+ public ScrollThread()\r
+ {\r
+ start();\r
+ }\r
+\r
+ public void setEvent(MouseEvent e)\r
+ {\r
+ evt = e;\r
+ }\r
+\r
+ public void stopScrolling()\r
+ {\r
+ running = false;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ running = true;\r
+ while (running)\r
+ {\r
+ if(evt!=null)\r
+ {\r
+\r
+ if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+ running = ap.scrollUp(true);\r
+\r
+ if (mouseDragging && evt.getY() >= getHeight() &&\r
+ av.alignment.getHeight() > av.getEndSeq())\r
+ running = ap.scrollUp(false);\r
+\r
+ if (mouseDragging && evt.getX() < 0)\r
+ running = ap.scrollRight(true);\r
+\r
+ else if (mouseDragging && evt.getX() >= getWidth())\r
+ running = ap.scrollRight(false);\r
+ }\r
+\r
+ try\r
+ {\r
+ Thread.sleep(75);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+ }\r
+}\r
+\r
+\r
\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff