\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
+import jalview.commands.*;\r
\r
import java.util.Vector;\r
\r
boolean mouseWheelPressed = false;\r
Point lastMousePress;\r
\r
+ EditCommand editCommand;\r
+\r
public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
{\r
this.av = avp;\r
\r
void endEditing()\r
{\r
+ if (editCommand!=null && editCommand.getSize() > 0)\r
+ {\r
+ ap.alignFrame.addHistoryItem(editCommand);\r
+ av.firePropertyChange("alignment", null,\r
+ av.getAlignment().getSequences());\r
+ }\r
+\r
startseq = -1;\r
lastres = -1;\r
- seqEditOccurred = false;\r
editingSeqs = false;\r
groupEditing = false;\r
keyboardNo1 = null;\r
keyboardNo2 = null;\r
+ editCommand = null;\r
}\r
\r
void setCursorRow()\r
{\r
seqCanvas.cursorX += dx;\r
seqCanvas.cursorY += dy;\r
+ if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))\r
+ {\r
+ int original = seqCanvas.cursorX - dx;\r
+ int maxWidth = av.alignment.getWidth();\r
+\r
+ while(!av.colSel.isVisible(seqCanvas.cursorX)\r
+ && seqCanvas.cursorX<maxWidth\r
+ && seqCanvas.cursorX>0)\r
+ {\r
+ seqCanvas.cursorX += dx;\r
+ }\r
+\r
+ if(seqCanvas.cursorX>=maxWidth\r
+ || !av.colSel.isVisible(seqCanvas.cursorX) )\r
+ {\r
+ seqCanvas.cursorX = original;\r
+ }\r
+ }\r
scrollToVisible();\r
}\r
\r
{\r
ap.scrollUp(false);\r
}\r
- while (seqCanvas.cursorX < av.startRes)\r
+ while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))\r
{\r
\r
if (!ap.scrollRight(false))\r
break;\r
}\r
- while (seqCanvas.cursorX > av.endRes)\r
+ while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))\r
{\r
if (!ap.scrollRight(true))\r
break;\r
SequenceGroup sg = av.selectionGroup;\r
//Find the top and bottom of this group\r
int min = av.alignment.getHeight(), max = 0;\r
- for(int i=0; i<sg.getSize(false); i++)\r
+ for(int i=0; i<sg.getSize(); i++)\r
{\r
int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
if(index > max)\r
else\r
{\r
// Now add any sequences between min and max\r
- sg.getSequences(false).removeAllElements();\r
+ sg.getSequences(null).removeAllElements();\r
for (int i = min; i < max; i++)\r
{\r
sg.addSequence(av.alignment.getSequenceAt(i), false);\r
\r
void insertGapAtCursor(boolean group)\r
{\r
- ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
- av.alignment, HistoryItem.EDIT));\r
groupEditing = group;\r
startseq = seqCanvas.cursorY;\r
lastres = seqCanvas.cursorX;\r
editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));\r
- editOccurred();\r
+ endEditing();\r
}\r
\r
void deleteGapAtCursor(boolean group)\r
{\r
- ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
- av.alignment, HistoryItem.EDIT));\r
groupEditing = group;\r
startseq = seqCanvas.cursorY;\r
lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);\r
editSequence(false, seqCanvas.cursorX);\r
- editOccurred();\r
+ endEditing();\r
}\r
\r
void numberPressed(char value)\r
{\r
lastMousePress = evt.getPoint();\r
\r
+ //For now, ignore the mouseWheel font resizing on Macs\r
+ //As the Button2_mask always seems to be true\r
if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==\r
InputEvent.BUTTON2_MASK && !av.MAC)\r
{\r
return;\r
}\r
\r
- if (evt.isShiftDown() || evt.isControlDown())\r
+ if (evt.isShiftDown()\r
+ || evt.isControlDown()\r
+ || evt.isAltDown())\r
{\r
- if (evt.isControlDown())\r
+ if (evt.isControlDown() || evt.isAltDown())\r
{\r
groupEditing = true;\r
}\r
if(seq<0 || res<0)\r
return;\r
\r
- ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
- av.alignment, HistoryItem.EDIT));\r
\r
if ((seq < av.getAlignment().getHeight()) &&\r
(res < av.getAlignment().getSequenceAt(seq).getLength()))\r
return;\r
}\r
\r
- editOccurred();\r
-\r
endEditing();\r
ap.repaint();\r
}\r
\r
\r
int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
+ if(cwidth<1)\r
+ return 0;\r
\r
wrappedBlock = y / cHeight;\r
wrappedBlock += av.getStartRes() / cwidth;\r
\r
public void doMousePressed(MouseEvent evt)\r
{\r
- ap.alignFrame.addHistoryItem(new HistoryItem(\r
- "Edit Sequence", av.alignment, HistoryItem.EDIT));\r
\r
int seq = findSeq(evt);\r
int res = findRes(evt);\r
\r
if (sf.getValue("status") != null )\r
{\r
- featureText.append(" (" + sf.getValue("status") + ")");\r
+ String status = sf.getValue("status").toString();\r
+ if(status.length()>0)\r
+ featureText.append(" (" + sf.getValue("status") + ")");\r
}\r
featureText.append("\n");\r
\r
tooltip.repaint();\r
\r
}\r
+ else if (tooltip != null)\r
+ {\r
+ tooltip.setTip("");\r
+ }\r
}\r
\r
Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
boolean fixedColumns = false;\r
SequenceGroup sg = av.getSelectionGroup();\r
\r
+ SequenceI seq = av.alignment.getSequenceAt(startseq);\r
\r
if (!groupEditing && av.hasHiddenRows)\r
{\r
- if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
+ if (av.hiddenRepSequences!=null\r
+ && av.hiddenRepSequences.containsKey(seq))\r
{\r
+ sg = (SequenceGroup)av.hiddenRepSequences.get(seq);\r
groupEditing = true;\r
- }\r
- }\r
-\r
- //No group, but the sequence may represent a group\r
- if (groupEditing\r
- && sg == null\r
- && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)\r
- {\r
- groupEditing = false;\r
+ }\r
}\r
\r
- SequenceI seq = av.alignment.getSequenceAt(startseq);\r
StringBuffer message = new StringBuffer();\r
if (groupEditing)\r
- message.append("Edit group:");\r
+ {\r
+ message.append("Edit group:");\r
+ if (editCommand == null)\r
+ editCommand = new EditCommand("Edit Group");\r
+ }\r
else\r
- message.append("Edit sequence: "+seq.getName());\r
+ {\r
+ message.append("Edit sequence: " + seq.getName());\r
+ String label = seq.getName();\r
+ if(label.length()>10)\r
+ label = label.substring(0,10);\r
+ if(editCommand==null)\r
+ editCommand = new EditCommand("Edit "+label);\r
+ }\r
\r
if(insertGap)\r
message.append(" insert ");\r
\r
//Are we editing within a selection group?\r
if (groupEditing\r
- || (sg != null && sg.getSequences(true).contains(seq)))\r
+ || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))\r
{\r
fixedColumns = true;\r
\r
//but the sequence represents a group\r
if (sg == null)\r
{\r
- sg = new SequenceGroup(null, null, false, false, false, 0,\r
- av.alignment.getWidth()-1);\r
- sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);\r
}\r
\r
fixedLeft = sg.getStartRes();\r
\r
if (groupEditing)\r
{\r
+ Vector vseqs = sg.getSequences(av.hiddenRepSequences);\r
+ int g, groupSize = vseqs.size();\r
+ SequenceI[] groupSeqs = new SequenceI[groupSize];\r
+ for (g = 0; g < groupSeqs.length; g++)\r
+ groupSeqs[g] = (SequenceI) vseqs.elementAt(g);\r
+\r
// drag to right\r
if (insertGap)\r
{\r
fixedRight--)\r
{\r
blank = true;\r
- for (int s = 0; s < sg.getSize(true); s++)\r
+\r
+ for (g = 0; g < groupSize; g++)\r
{\r
- seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
for (int j = 0; j < startres - lastres; j++)\r
{\r
if (!jalview.util.Comparison.isGap(\r
- seq.getCharAt(fixedRight - j)))\r
+ groupSeqs[g].getCharAt(fixedRight - j)))\r
{\r
blank = false;\r
break;\r
\r
if (!blank)\r
{\r
- if(sg.getSize(false) == av.alignment.getHeight() )\r
+ if(sg.getSize() == av.alignment.getHeight() )\r
{\r
if((av.hasHiddenColumns\r
&& startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
/// Are we able to delete?\r
// ie are all columns blank?\r
\r
- for (int s = 0; s < sg.getSize(true); s++)\r
+ for (g = 0; g < groupSize; g++)\r
{\r
- seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
-\r
for (int j = startres; j < lastres; j++)\r
{\r
- if (seq.getSequence().length() <= j)\r
+ if (groupSeqs[g].getLength() <= j)\r
{\r
continue;\r
}\r
\r
if (!jalview.util.Comparison.isGap(\r
- seq.getSequence().charAt(j)))\r
+ groupSeqs[g].getCharAt(j)))\r
{\r
// Not a gap, block edit not valid\r
endEditing();\r
}\r
}\r
\r
-\r
- for (int i = 0; i < sg.getSize(true); i++)\r
- {\r
- seq = (SequenceI) sg.getSequences(true).elementAt(i);\r
-\r
if (insertGap)\r
{\r
// dragging to the right\r
- for (int j = lastres; j < startres; j++)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j < startres; j++)\r
{\r
- insertChar(j, seq, fixedRight);\r
+ insertChar(j, groupSeqs, fixedRight);\r
}\r
- else\r
- insertChar(j, seq);\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ groupSeqs,\r
+ startres, startres-lastres,\r
+ av.getGapCharacter(),\r
+ true);\r
}\r
}\r
else\r
{\r
// dragging to the left\r
- for (int j = lastres; j > startres; j--)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- deleteChar(startres, seq, fixedRight);\r
- }\r
- else\r
+ for (int j = lastres; j > startres; j--)\r
{\r
- deleteChar(startres, seq);\r
+ deleteChar(startres, groupSeqs, fixedRight);\r
}\r
}\r
+ else\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ groupSeqs,\r
+ startres, lastres - startres,\r
+ av.getGapCharacter(),\r
+ true);\r
+\r
}\r
- }\r
}\r
else /////Editing a single sequence///////////\r
{\r
if (insertGap)\r
{\r
// dragging to the right\r
- for (int j = lastres; j < startres; j++)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j < startres; j++)\r
{\r
- insertChar(j, seq, fixedRight);\r
+ insertChar(j, new SequenceI[]{seq}, fixedRight);\r
}\r
- else\r
- insertChar(j, seq);\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ new SequenceI[]\r
+ {seq},\r
+ lastres, startres-lastres,\r
+ av.getGapCharacter(),\r
+ true);\r
}\r
}\r
else\r
{\r
// dragging to the left\r
- for (int j = lastres; j > startres; j--)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j > startres; j--)\r
{\r
- deleteChar(startres, seq, fixedRight);\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
+ {\r
+ endEditing();\r
+ break;\r
+ }\r
+ deleteChar(startres, new SequenceI[]{seq}, fixedRight);\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ //could be a keyboard edit trying to delete none gaps\r
+ int max=0;\r
+ for(int m = startres; m<lastres; m++)\r
{\r
- deleteChar(startres, seq);\r
+ if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))\r
+ break;\r
+ max++;\r
+ }\r
+\r
+ if (max>0)\r
+ {\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ new SequenceI[]\r
+ {seq},\r
+ startres, max,\r
+ av.getGapCharacter(),\r
+ true);\r
}\r
}\r
}\r
}\r
\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param j DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- void insertChar(int j, SequenceI seq)\r
- {\r
- seq.insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = true;\r
- }\r
\r
- void insertChar(int j, SequenceI seq, int fixedColumn)\r
+ void insertChar(int j, SequenceI [] seq, int fixedColumn)\r
+ {\r
+ int blankColumn = fixedColumn;\r
+ for(int s=0; s<seq.length; s++)\r
{\r
//Find the next gap before the end of the visible region boundary\r
//If lastCol > j, theres a boundary after the gap insertion\r
- int blankColumn = fixedColumn;\r
+\r
for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
{\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
+ if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))\r
{\r
//Theres a space, so break and insert the gap\r
break;\r
\r
if (blankColumn <= j)\r
{\r
+ blankColumn = fixedColumn;\r
endEditing();\r
return;\r
}\r
-\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
- {\r
- //Just Checking\r
- System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));\r
- return;\r
- }\r
-\r
- seq.deleteCharAt(blankColumn);\r
- seq.insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = true;\r
}\r
\r
- void deleteChar(int j, SequenceI seq, int fixedColumn)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
- {\r
- ap.alignFrame.statusBar.setText(\r
- "End editing: Tried removing residue " + seq.getCharAt(j));\r
- return;\r
- }\r
-\r
- seq.deleteCharAt(j);\r
- seq.insertCharAt(fixedColumn, av.getGapCharacter());\r
- seqEditOccurred = true;\r
- }\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ seq,\r
+ blankColumn, 1, av.getGapCharacter(), true);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param j DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- void deleteChar(int j, SequenceI seq)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
- {\r
- ap.alignFrame.statusBar.setText(\r
- "End editing: Tried removing residue " + seq.getCharAt(j));\r
- return;\r
- }\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ seq,\r
+ j, 1, av.getGapCharacter(),\r
+ true);\r
\r
- seq.deleteCharAt(j);\r
- seqEditOccurred = true;\r
- seqCanvas.repaint();\r
- }\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- void editOccurred()\r
- {\r
- if (!seqEditOccurred)\r
- {\r
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\r
- }\r
+ void deleteChar(int j, SequenceI [] seq, int fixedColumn)\r
+ {\r
\r
- endEditing();\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ seq,\r
+ j, 1, av.getGapCharacter(), true);\r
\r
- av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ seq,\r
+ fixedColumn, 1, av.getGapCharacter(), true);\r
+ }\r
\r
- }\r
\r
//////////////////////////////////////////\r
/////Everything below this is for defining the boundary of the rubberband\r
//////////////////////////////////////////\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
-\r
-\r
if (scrollThread != null)\r
{\r
scrollThread.running = false;\r
}\r
}\r
\r
- else if (!stretchGroup.getSequences(false).contains(sequence)\r
+ else if (!stretchGroup.getSequences(null).contains(sequence)\r
|| stretchGroup.getStartRes() > res\r
|| stretchGroup.getEndRes() < res)\r
{\r
if (stretchGroup.cs instanceof ClustalxColourScheme)\r
{\r
( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
- stretchGroup.getSequences(true),\r
+ stretchGroup.getSequences(av.hiddenRepSequences),\r
stretchGroup.getWidth());\r
}\r
\r
+ if (stretchGroup.cs instanceof Blosum62ColourScheme\r
+ || stretchGroup.cs instanceof PIDColourScheme\r
+ || stretchGroup.cs.conservationApplied()\r
+ || stretchGroup.cs.getThreshold() > 0)\r
+ stretchGroup.recalcConservation();\r
+\r
+\r
if (stretchGroup.cs.conservationApplied())\r
{\r
SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
- PaintRefresher.Refresh(av.alignment);\r
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());\r
ap.repaint();\r
}\r
\r
y = av.alignment.getHeight() -1;\r
}\r
\r
- if(res>av.alignment.getWidth())\r
+ if(res>=av.alignment.getWidth())\r
res = av.alignment.getWidth()-1;\r
\r
if (stretchGroup.getEndRes() == res)\r
\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
- if (stretchGroup.getSequences(false).contains(nextSeq))\r
+ if (stretchGroup.getSequences(null).contains(nextSeq))\r
{\r
stretchGroup.deleteSequence(seq, false);\r
}\r
git://source.jalview.org / jalview.git / blobdiff