+/*\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.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
+\r
import jalview.datamodel.*;\r
-import java.util.*;\r
import jalview.schemes.*;\r
\r
-\r
-public class SeqPanel extends Panel\r
+public class SeqPanel\r
+ extends Panel\r
{\r
\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
+ public SeqCanvas seqCanvas;\r
+ public AlignmentPanel ap;\r
\r
protected int lastres;\r
protected int startseq;\r
+ int startEdit = -1;\r
+ int endEdit = -1;\r
\r
protected AlignViewport av;\r
\r
ScrollThread scrollThread = null;\r
boolean mouseDragging = false;\r
\r
+ boolean editingSeqs = false;\r
+ boolean groupEditing = false;\r
\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
- this.av = avp;\r
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+ {\r
+ this.av = avp;\r
\r
- seqCanvas = new SeqCanvas(avp);\r
+ seqCanvas = new SeqCanvas(avp);\r
setLayout(new BorderLayout());\r
add(seqCanvas);\r
\r
ap = p;\r
\r
- seqCanvas.addMouseMotionListener( new MouseMotionAdapter()\r
+ seqCanvas.addMouseMotionListener(new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- doMouseMoved(evt); }\r
+ doMouseMoved(evt);\r
+ }\r
\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if (editingSeqs)\r
+ {\r
doMouseDragged(evt);\r
+ }\r
else\r
+ {\r
doMouseDraggedDefineMode(evt);\r
+ }\r
}\r
});\r
\r
- seqCanvas.addMouseListener( new MouseAdapter()\r
+ seqCanvas.addMouseListener(new MouseAdapter()\r
{\r
public void mouseReleased(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if (editingSeqs)\r
+ {\r
doMouseReleased(evt);\r
+ }\r
else\r
+ {\r
doMouseReleasedDefineMode(evt);\r
+ }\r
+\r
}\r
+\r
public void mousePressed(MouseEvent evt)\r
{\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ groupEditing = true;\r
+ }\r
+\r
+ editingSeqs = true;\r
doMousePressed(evt);\r
+ }\r
else\r
+ {\r
doMousePressedDefineMode(evt);\r
+ }\r
}\r
+\r
public void mouseExited(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
- return;\r
- doMouseExitedDefineMode(evt);\r
+ if (editingSeqs)\r
+ {\r
+ return;\r
+ }\r
+ doMouseExitedDefineMode(evt);\r
\r
}\r
+\r
public void mouseEntered(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
+ if (editingSeqs)\r
+ {\r
return;\r
+ }\r
doMouseEnteredDefineMode(evt);\r
}\r
\r
seqCanvas.repaint();\r
}\r
\r
+ public void doMouseReleased(MouseEvent evt)\r
+ {\r
\r
- public void doMouseReleased(MouseEvent evt) {\r
+ if (seqEditOccurred > -1)\r
+ {\r
+ editOccurred(seqEditOccurred);\r
+ }\r
\r
startseq = -1;\r
- lastres = -1;\r
- if(seqEditOccurred>-1)\r
- updateConservation(seqEditOccurred);\r
-\r
+ lastres = -1;\r
seqEditOccurred = -1;\r
-\r
+ editingSeqs = false;\r
+ groupEditing = false;\r
ap.repaint();\r
}\r
\r
- public void doMousePressed(MouseEvent evt) {\r
- ap.alignFrame.addHistoryItem("sequence edit");\r
- int seq;\r
- int res;\r
+ int findRes(MouseEvent evt)\r
+ {\r
+ int res = 0;\r
+ int x = evt.getX();\r
+\r
+ if (av.wrapAlignment)\r
+ {\r
+ int y = evt.getY();\r
+ y -= (2 * av.charHeight);\r
+ x -= seqCanvas.LABEL_WEST;\r
\r
- int x = evt.getX();\r
- int y = evt.getY();\r
+ int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);\r
+ int block = y/chunkHeight;\r
+ block += av.getStartRes()/cwidth;\r
+\r
+ res = block*cwidth + x / av.getCharWidth();\r
+ }\r
+ else\r
+ {\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
+ }\r
+\r
+ return res;\r
+\r
+ }\r
+\r
+ int findSeq(MouseEvent evt)\r
+ {\r
+ int seq = 0;\r
+ int y = evt.getY();\r
+\r
+ if (av.wrapAlignment)\r
+ {\r
+ y -= (2 * av.charHeight);\r
+ int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ seq = ( (y % chunkHeight) / av.getCharHeight());\r
+ }\r
+ else\r
+ {\r
+ seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+\r
+ public void doMousePressed(MouseEvent evt)\r
+ {\r
+ ap.alignFrame.addHistoryItem(new HistoryItem(\r
+ "Edit Sequence", av.alignment, HistoryItem.EDIT));\r
\r
- res = x/av.getCharWidth() + av.getStartRes();\r
- seq = y/av.getCharHeight() + av.getStartSeq();\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
\r
if (seq < av.getAlignment().getHeight() &&\r
res < av.getAlignment().getSequenceAt(seq).getLength())\r
\r
public void doMouseMoved(MouseEvent evt)\r
{\r
- int res=0, seq=0;\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- if(av.wrapAlignment)\r
- {\r
- y -= 2*av.charHeight;\r
- int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
-\r
-\r
- res = (int)((y/chunkHeight)*(getSize().width/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
\r
- y %= chunkHeight;\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
-\r
- }\r
- else\r
+ if (seq >= av.getAlignment().getHeight())\r
{\r
- res = x / av.getCharWidth() + av.getStartRes();\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
- }\r
-\r
-\r
- if(seq>=av.getAlignment().getHeight())\r
return;\r
+ }\r
\r
SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
- if(res>sequence.getLength())\r
+ if (res > sequence.getLength())\r
+ {\r
return;\r
+ }\r
\r
- Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
+ Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
String aa = "";\r
- if(obj!=null)\r
- aa = obj.toString();\r
+ if (obj != null)\r
+ {\r
+ aa = obj.toString();\r
+ }\r
\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
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
+ if (aa != "")\r
+ {\r
+ text.append(" Residue: " + aa + " (" +\r
+ av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+ }\r
\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
+ 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
+ if (sbuffer.length() > 0)\r
+ {\r
sbuffer.append("; ");\r
+ }\r
sbuffer.append(sf.getType() + " " + sf.getDescription());\r
- if(sf.getStatus().length()>0)\r
- sbuffer.append(" ("+sf.getStatus()+")");\r
+ if (sf.getStatus().length() > 0)\r
+ {\r
+ sbuffer.append(" (" + sf.getStatus() + ")");\r
+ }\r
}\r
\r
}\r
}\r
\r
-\r
}\r
\r
- public void doMouseDragged(MouseEvent evt) {\r
-\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
+ public void doMouseDragged(MouseEvent evt)\r
+ {\r
\r
- if (lastres == -1 || lastres == res)\r
- return;\r
+ // If we're dragging we're editing\r
+ int res = findRes(evt);\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
\r
- boolean dragRight = true;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- dragRight = false;\r
+ if (lastres == -1 || lastres == res)\r
+ {\r
+ return;\r
+ }\r
\r
+ boolean dragRight = true;\r
+ if (res < av.getAlignment().getWidth() && res < lastres)\r
+ {\r
+ dragRight = false;\r
+ }\r
\r
- if (res != lastres)\r
+ if (res != lastres)\r
+ {\r
+ // Group editing\r
+ if (groupEditing)\r
{\r
- // Group editing\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg==null)\r
- {\r
- lastres=-1;\r
- return;\r
- }\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ lastres = -1;\r
+ return;\r
+ }\r
\r
- // drag to right\r
- if(dragRight)\r
- sg.setEndRes(sg.getEndRes() + (res-lastres));\r
+ // drag to right\r
+ if (dragRight)\r
+ {\r
+ sg.setEndRes(sg.getEndRes() + (res - lastres));\r
+ }\r
\r
- // drag to left\r
- else\r
+ // drag to left\r
+ else\r
+ {\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 seq = sg.getSequenceAt(s);\r
+ for (int j = res; j < lastres; j++)\r
+ {\r
+ if (seq.getSequence().length() <= j)\r
{\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 seq = sg.getSequenceAt(s);\r
- for (int j=res; j<lastres; j++)\r
- {\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
- if(!deleteAllowed)\r
- {\r
- lastres = -1;\r
- return;\r
- }\r
-\r
- sg.setEndRes(sg.getEndRes() - (lastres-res));\r
+ continue;\r
}\r
\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
{\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
-\r
- // drag to right\r
- if (dragRight)\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, k);\r
-\r
- // drag to left\r
- else\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if(s.getLength()>j)\r
- deleteChar(res, k);\r
- }\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
- else /////Editing a single sequence///////////\r
+\r
+ if (!deleteAllowed)\r
{\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
+ lastres = -1;\r
+ return;\r
+ }\r
+\r
+ sg.setEndRes(sg.getEndRes() - (lastres - res));\r
+ }\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI s = sg.getSequenceAt(i);\r
+ int k = av.alignment.findIndex(s);\r
+\r
+ // drag to right\r
+ if (dragRight)\r
+ {\r
+ for (int j = lastres; j < res; j++)\r
{\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, startseq);\r
+ insertChar(j, k);\r
}\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\r
+ }\r
+\r
+ // drag to left\r
+ else\r
+ {\r
+ for (int j = res; j < lastres; j++)\r
{\r
- // dragging to the left\r
- for (int j = lastres; j > res; j--)\r
+ if (s.getLength() > j)\r
{\r
- deleteChar(res, startseq);\r
+ deleteChar(res, k);\r
}\r
}\r
+ }\r
+ }\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+ if (res < av.getAlignment().getWidth() && res > lastres)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < res; j++)\r
+ {\r
+ insertChar(j, startseq);\r
+ }\r
+ }\r
+ else if (res < av.getAlignment().getWidth() && res < lastres)\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > res; j--)\r
+ {\r
+ if (jalview.util.Comparison.isGap(\r
+ av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
+ {\r
+\r
+ deleteChar(res, startseq);\r
+ }\r
+ else\r
+ {\r
\r
+ break;\r
+ }\r
}\r
+ }\r
+\r
}\r
+ }\r
\r
- lastres = res;\r
- seqCanvas.repaint();\r
+ endEdit = res;\r
+ lastres = res;\r
+ seqCanvas.repaint();\r
}\r
\r
- public void drawChars(int seqstart, int seqend, int start) {\r
- seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);\r
+ public void drawChars(int seqstart, int seqend, int start)\r
+ {\r
+ seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,\r
+ av.getStartRes(), av.getStartSeq(), 0);\r
seqCanvas.repaint();\r
}\r
\r
public void insertChar(int j, int seq)\r
{\r
av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred=seq;\r
+ seqEditOccurred = seq;\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
-\r
+ av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+ seqEditOccurred = seq;\r
av.alignment.getWidth();\r
repaint();\r
- seqEditOccurred=seq;\r
}\r
\r
-\r
- void updateConservation(int i)\r
+ void editOccurred(int i)\r
{\r
+ if (endEdit == startEdit)\r
+ {\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
av.updateConservation();\r
av.updateConsensus();\r
\r
+\r
+ //Does the edit affect any groups?\r
+ //////////////////////////////\r
+ Vector groupsToUpdate = new Vector();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+\r
+ int s, g, gSize = av.alignment.getGroups().size();\r
+ if (sg != null)\r
+ {\r
+ groupsToUpdate.addElement(av.getSelectionGroup());\r
+ int sSize = sg.getSize();\r
+ for (s = 0; s < sSize; s++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(s);\r
+\r
+ for (g = 0; g < gSize; g++)\r
+ {\r
+ SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().\r
+ elementAt(\r
+ g);\r
+ if (sg2.sequences.contains(seq))\r
+ {\r
+ if (!groupsToUpdate.contains(sg2))\r
+ groupsToUpdate.addElement(sg2);\r
+ continue;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(startseq);\r
+ for (g = 0; g < gSize; g++)\r
+ {\r
+ SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(\r
+ g);\r
+ if (sg2.sequences.contains(seq))\r
+ {\r
+ if (!groupsToUpdate.contains(sg2))\r
+ groupsToUpdate.addElement(sg2);\r
+ continue;\r
+ }\r
+ }\r
+ }\r
+\r
+ gSize = groupsToUpdate.size();\r
+ for (g = 0; g < gSize; g++)\r
+ {\r
+ ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();\r
+ }\r
+ ////End of updating groups\r
+ //////////////////////////////////////////\r
+\r
+\r
+ // Y O Y CLUSTALX\r
ColourSchemeI cs = av.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme)\r
- cs = ( (ConservationColourScheme) cs).cs;\r
\r
- if(cs instanceof ClustalxColourScheme)\r
- cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());\r
+ if (av.getSelectionGroup() != null)\r
+ {\r
+ av.getSelectionGroup().recalcConservation();\r
+ }\r
\r
- ap.alignFrame.changeColour(cs);\r
+ if(cs!=null)\r
+ {\r
+ if (cs.conservationApplied())\r
+ {\r
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ av.alignment.getSequences(),\r
+ 0, av.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
+ cxs.resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
+ cs.setConservation(c);\r
+ av.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(c);\r
+ av.setGlobalColourScheme(cs);\r
+ }\r
+\r
+ }\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
+ av.alignment.getWidth());\r
+ av.setGlobalColourScheme(cs);\r
+ }\r
+ }\r
}\r
\r
//////////////////////////////////////////\r
int oldSeq = -1;\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
oldSeq = seq;\r
\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
- if(sequence==null || res>sequence.getLength())\r
+ if (sequence == null || res > sequence.getLength())\r
+ {\r
return;\r
+ }\r
\r
stretchGroup = av.getSelectionGroup();\r
\r
- if(stretchGroup == null)\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
+ if (stretchGroup == null)\r
+ {\r
+ stretchGroup = av.alignment.findGroup(sequence);\r
+ if (stretchGroup != null && res > stretchGroup.getStartRes() &&\r
+ res < stretchGroup.getEndRes())\r
+ {\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup = null;\r
+ }\r
+ }\r
\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 );\r
-\r
- if (allGroups != null)\r
- for (int i = 0; i < allGroups.length; i++)\r
- if (allGroups[i].getStartRes() <= res &&\r
- allGroups[i].getEndRes() >= res)\r
- {\r
- stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
- break;\r
- }\r
- }\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);\r
+\r
+ if (allGroups != null)\r
+ {\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if (allGroups[i].getStartRes() <= res &&\r
+ allGroups[i].getEndRes() >= res)\r
+ {\r
+ stretchGroup = allGroups[i];\r
+ av.setSelectionGroup(stretchGroup);\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
{\r
// define a new group here\r
SequenceGroup sg = new SequenceGroup();\r
sg.setStartRes(res);\r
sg.setEndRes(res);\r
- sg.addSequence( sequence );\r
- av.setSelectionGroup( sg );\r
+ sg.addSequence(sequence, false);\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
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
\r
}\r
\r
// DETECT RIGHT MOUSE BUTTON IN AWT\r
- else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )\r
+ else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
+ InputEvent.BUTTON3_MASK)\r
{\r
- APopupMenu popup = new APopupMenu(ap, null);\r
+ APopupMenu popup = new APopupMenu(ap, null, null);\r
this.add(popup);\r
popup.show(this, evt.getX(), evt.getY());\r
}\r
\r
-\r
- if(stretchGroup!=null && stretchGroup.getEndRes()==res)\r
+ if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
+ {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
+ }\r
\r
- else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
+ else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
+ {\r
// Edit end res position of selected group\r
changeStartRes = true;\r
+ }\r
\r
}\r
\r
\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
- mouseDragging = false;\r
-\r
- if(stretchGroup==null)\r
- return;\r
+ if(mouseDragging)\r
+ {\r
+ stretchGroup.recalcConservation();\r
+ mouseDragging = false;\r
+ }\r
\r
- if(stretchGroup.cs instanceof ClustalxColourScheme)\r
+ if (stretchGroup == null)\r
{\r
- stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
- seqCanvas.repaint();\r
+ return;\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
- seqCanvas.repaint();\r
- }\r
- else\r
+ if(stretchGroup.cs!=null)\r
{\r
- if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())\r
+ if (stretchGroup.cs.conservationApplied())\r
{\r
- ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;\r
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
+ }\r
+ else\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
}\r
-\r
}\r
-\r
-\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
+ seqCanvas.repaint();\r
ap.repaint();\r
}\r
\r
-\r
boolean remove = false;\r
public void doMouseDraggedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ int res = findRes(evt);\r
+ int y = findSeq(evt);\r
\r
- if(stretchGroup==null)\r
+ if (stretchGroup == null)\r
+ {\r
return;\r
+ }\r
\r
- if(res>av.alignment.getWidth())\r
- res = av.alignment.getWidth()-1;\r
-\r
+ if (res > av.alignment.getWidth())\r
+ {\r
+ res = av.alignment.getWidth() - 1;\r
+ }\r
\r
- if(stretchGroup.getEndRes()==res)\r
+ if (stretchGroup.getEndRes() == res)\r
+ {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
+ }\r
\r
- else if(stretchGroup.getStartRes()==res)\r
+ else if (stretchGroup.getStartRes() == res)\r
+ {\r
// Edit start res position of selected group\r
changeStartRes = true;\r
+ }\r
\r
-\r
- if(res<av.getStartRes())\r
+ if (res < av.getStartRes())\r
+ {\r
res = av.getStartRes();\r
- else if(res>av.getEndRes())\r
+ }\r
+ else if (res > av.getEndRes() && !av.getWrapAlignment())\r
+ {\r
res = av.getEndRes();\r
+ }\r
\r
- if(changeEndRes)\r
+ if (changeEndRes)\r
{\r
- if(res>stretchGroup.getStartRes()-1)\r
- stretchGroup.setEndRes( res );\r
+ if (res > stretchGroup.getStartRes() - 1)\r
+ {\r
+ stretchGroup.setEndRes(res);\r
+ }\r
}\r
- else if(changeStartRes)\r
+ else if (changeStartRes)\r
{\r
- if(res<stretchGroup.getEndRes()+1)\r
- stretchGroup.setStartRes( res );\r
+ if (res < stretchGroup.getEndRes() + 1)\r
+ {\r
+ stretchGroup.setStartRes(res);\r
+ }\r
}\r
\r
int dragDirection = 0;\r
if (y > oldSeq)\r
+ {\r
dragDirection = 1;\r
+ }\r
else if (y < oldSeq)\r
+ {\r
dragDirection = -1;\r
+ }\r
\r
- while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\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
if (stretchGroup.sequences.contains(nextSeq))\r
{\r
- stretchGroup.deleteSequence(seq);\r
- stretchGroup.deleteSequence(nextSeq);\r
+ stretchGroup.deleteSequence(seq, false);\r
}\r
else\r
{\r
- if(seq!=null)\r
- stretchGroup.addSequence(seq);\r
- stretchGroup.addSequence(nextSeq);\r
+ if (seq != null)\r
+ {\r
+ stretchGroup.addSequence(seq, false);\r
+ }\r
+ stretchGroup.addSequence(nextSeq, false);\r
}\r
}\r
oldSeq = y;\r
mouseDragging = true;\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.setEvent(evt);\r
+ }\r
\r
seqCanvas.repaint();\r
}\r
public void doMouseEnteredDefineMode(MouseEvent e)\r
{\r
if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
}\r
\r
public void doMouseExitedDefineMode(MouseEvent e)\r
{\r
- if (av.getWrapAlignment())\r
- return;\r
-\r
- if(mouseDragging)\r
+ if (mouseDragging)\r
+ {\r
scrollThread = new ScrollThread();\r
+ }\r
\r
}\r
+\r
// this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread extends Thread\r
+ class ScrollThread\r
+ extends Thread\r
{\r
MouseEvent evt;\r
boolean running = false;\r
running = true;\r
while (running)\r
{\r
- if(evt!=null)\r
+ if (evt != null)\r
{\r
\r
if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+ {\r
running = ap.scrollUp(true);\r
+ }\r
\r
if (mouseDragging && evt.getY() >= getSize().height &&\r
av.alignment.getHeight() > av.getEndSeq())\r
+ {\r
running = ap.scrollUp(false);\r
+ }\r
\r
if (mouseDragging && evt.getX() < 0)\r
+ {\r
running = ap.scrollRight(true);\r
+ }\r
\r
else if (mouseDragging && evt.getX() >= getSize().width)\r
+ {\r
running = ap.scrollRight(false);\r
+ }\r
}\r
\r
try\r
{}\r
}\r
}\r
-}\r
-\r
-\r
+ }\r
\r
}\r
-\r
-\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff