+/*\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 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
public SeqCanvas seqCanvas;\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
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
if(av.getWrapAlignment())\r
return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if( editingSeqs )\r
doMouseDragged(evt);\r
else\r
doMouseDraggedDefineMode(evt);\r
{\r
if(av.getWrapAlignment())\r
return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\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() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
+ if (av.getWrapAlignment() || editingSeqs)\r
return;\r
doMouseExitedDefineMode(evt);\r
\r
}\r
public void mouseEntered(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
+ if (av.getWrapAlignment() || editingSeqs)\r
return;\r
doMouseEnteredDefineMode(evt);\r
}\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
- ap.RefreshPanels();\r
- repaint();\r
-\r
+ ap.repaint();\r
}\r
\r
public void doMousePressed(MouseEvent evt) {\r
- ap.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
}\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
\r
- if(lastres==-1)\r
+ if (lastres == -1 || lastres == res)\r
return;\r
\r
- int x = evt.getX();\r
+ boolean dragRight = true;\r
+ if (res < av.getAlignment().getWidth() && res < lastres)\r
+ dragRight = false;\r
\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
- if (res < 0)\r
- res = 0;\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.getSelectionGroup();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
if(sg==null)\r
- av.getAlignment().findGroup(startseq);\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
+ 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
+ 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
stretchGroup = sg;\r
\r
if(av.getConservationSelected())\r
- Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
- else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();\r
- int threshold = rcs.getThreshold();\r
- if (threshold > 0)\r
- Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
- }\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
// Edit end res position of selected group\r
changeStartRes = true;\r
\r
+ stretchGroup.getWidth();\r
\r
repaint();\r
\r
\r
else if(stretchGroup.cs instanceof ConservationColourScheme)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
-\r
-\r
+ ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
stretchGroup.cs = ccs;\r
-\r
-\r
- Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
\r
repaint();\r
}\r
else\r
- {\r
- if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;\r
- int threshold = rcs.getThreshold();\r
- if(threshold>0)\r
- Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
- }\r
-\r
- }\r
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
\r
\r
changeEndRes = false;\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
else if (y < oldSeq)\r
dragDirection = -1;\r
\r
- while (y != oldSeq && oldSeq>0)\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
git://source.jalview.org / jalview.git / blobdiff