boolean remove = false;\r
\r
boolean mouseWheelPressed = false;\r
+ StringBuffer keyboardNo1;\r
+ StringBuffer keyboardNo2;\r
\r
/**\r
* Creates a new SeqPanel object.\r
seqEditOccurred = false;\r
editingSeqs = false;\r
groupEditing = false;\r
- keyboardGaps = null;\r
+ keyboardNo1 = null;\r
+ keyboardNo2 = null;\r
}\r
\r
+ void setCursorRow()\r
+ {\r
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;\r
+ scrollToVisible();\r
+ }\r
+\r
+ void setCursorColumn()\r
+ {\r
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;\r
+ scrollToVisible();\r
+ }\r
+\r
+ void setCursorRowAndColumn()\r
+ {\r
+ if(keyboardNo2==null)\r
+ {\r
+ keyboardNo2 = new StringBuffer();\r
+ }\r
+ else\r
+ {\r
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;\r
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;\r
+ scrollToVisible();\r
+ }\r
+ }\r
+\r
+ void setCursorPosition()\r
+ {\r
+ SequenceI sequence =\r
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
+\r
+ seqCanvas.cursorX = sequence.findIndex(\r
+ getKeyboardNo(keyboardNo1)-1\r
+ );\r
+ scrollToVisible();\r
+ }\r
\r
void moveCursor(int dx, int dy)\r
{\r
seqCanvas.cursorX += dx;\r
seqCanvas.cursorY += dy;\r
+ scrollToVisible();\r
+ }\r
\r
- if(seqCanvas.cursorX<0)\r
+ void scrollToVisible()\r
+ {\r
+ if (seqCanvas.cursorX < 0)\r
seqCanvas.cursorX = 0;\r
- else if(seqCanvas.cursorX>av.alignment.getWidth()-1)\r
- seqCanvas.cursorX = av.alignment.getWidth()-1;\r
- if(seqCanvas.cursorX<av.startRes)\r
- ap.scrollRight(false);\r
- else if(seqCanvas.cursorX>av.endRes)\r
- ap.scrollRight(true);\r
-\r
- if(seqCanvas.cursorY<0)\r
- seqCanvas.cursorY=0;\r
- else if(seqCanvas.cursorY>av.alignment.getHeight()-1)\r
- seqCanvas.cursorY = av.alignment.getHeight()-1;\r
- if(seqCanvas.cursorY<av.startSeq)\r
+ else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)\r
+ seqCanvas.cursorX = av.alignment.getWidth() - 1;\r
+\r
+ if (seqCanvas.cursorY < 0)\r
+ seqCanvas.cursorY = 0;\r
+ else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)\r
+ seqCanvas.cursorY = av.alignment.getHeight() - 1;\r
+\r
+\r
+ endEditing();\r
+ while (seqCanvas.cursorY < av.startSeq)\r
+ {\r
ap.scrollUp(true);\r
- else if(seqCanvas.cursorY+1>av.endSeq)\r
+ }\r
+ while (seqCanvas.cursorY + 1 > av.endSeq)\r
+ {\r
ap.scrollUp(false);\r
+ }\r
+ while (seqCanvas.cursorX < av.startRes)\r
+ {\r
+ if(!ap.scrollRight(false))\r
+ break;\r
+ }\r
+ while (seqCanvas.cursorX > av.endRes)\r
+ {\r
+ if(!ap.scrollRight(true))\r
+ break;\r
+ }\r
\r
setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
seqCanvas.cursorX, seqCanvas.cursorY);\r
+\r
seqCanvas.repaint();\r
}\r
\r
groupEditing = group;\r
startseq = seqCanvas.cursorY;\r
lastres = seqCanvas.cursorX;\r
- editSequence(true, seqCanvas.cursorX+getKeyboardGaps());\r
+ editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));\r
editOccurred();\r
}\r
\r
av.alignment, HistoryItem.EDIT));\r
groupEditing = group;\r
startseq = seqCanvas.cursorY;\r
- lastres = seqCanvas.cursorX+getKeyboardGaps();\r
+ lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);\r
editSequence(false, seqCanvas.cursorX);\r
editOccurred();\r
}\r
\r
void numberPressed(char value)\r
{\r
- if(keyboardGaps==null)\r
- keyboardGaps = new StringBuffer();\r
+ if(keyboardNo1==null)\r
+ keyboardNo1 = new StringBuffer();\r
\r
- keyboardGaps.append(value);\r
+ if(keyboardNo2!=null)\r
+ keyboardNo2.append(value);\r
+ else\r
+ keyboardNo1.append(value);\r
}\r
\r
- StringBuffer keyboardGaps;\r
- int getKeyboardGaps()\r
+ int getKeyboardNo(StringBuffer kb)\r
{\r
- if(keyboardGaps==null)\r
+ if(kb==null)\r
return 1;\r
else\r
- return Integer.parseInt(keyboardGaps.toString());\r
+ return Integer.parseInt(kb.toString());\r
}\r
\r
\r
\r
}\r
\r
- void editSequence(boolean insertGap, int startres)\r
+ synchronized void editSequence(boolean insertGap, int startres)\r
{\r
int fixedLeft = -1;\r
int fixedRight = -1;\r
boolean fixedColumns = false;\r
+ SequenceGroup sg = av.getSelectionGroup();\r
\r
- if(insertGap && av.hasHiddenColumns)\r
- {\r
- //Stop editing if the user has dragged beyond hiddenBoundary\r
- fixedRight = av.getColumnSelection().getHiddenRegionBoundary(lastres);\r
- if( fixedRight < lastres)\r
- {\r
- if(lastres!=fixedRight)\r
- {\r
- endEditing();\r
- return;\r
- }\r
- }\r
- }\r
+ if(groupEditing && sg==null)\r
+ return;\r
\r
if (!groupEditing && av.hasHiddenRows)\r
{\r
+ //This needs to check all the sequences in a group edit,m\r
+ // not just the startseq\r
if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
{\r
groupEditing = true;\r
}\r
}\r
\r
-\r
SequenceI seq = av.alignment.getSequenceAt(startseq);\r
StringBuffer message = new StringBuffer();\r
if (groupEditing)\r
- message.append("Edit group:");\r
- else\r
+ message.append("Edit group:");\r
+ else\r
message.append("Edit sequence: "+seq.getName());\r
\r
if(insertGap)\r
\r
//Are we editing within a selection group?\r
if (groupEditing\r
- || (av.getSelectionGroup() != null &&\r
- av.getSelectionGroup().sequences.contains(seq)))\r
+ || (sg != null && sg.sequences.contains(seq)))\r
{\r
fixedColumns = true;\r
\r
- fixedLeft = av.getSelectionGroup().getStartRes();\r
- fixedRight = av.getSelectionGroup().getEndRes();\r
+ fixedLeft = sg.getStartRes();\r
+ fixedRight = sg.getEndRes();\r
\r
if ( (startres < fixedLeft && lastres >= fixedLeft)\r
|| (startres >= fixedLeft && lastres < fixedLeft)\r
}\r
}\r
\r
+\r
+\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ fixedColumns = true;\r
+ int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
+ int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
+\r
+ if( ( insertGap && startres>y1 && lastres<y1)\r
+ || (!insertGap && startres<y2 && lastres>y2) )\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if(fixedRight<y2 && fixedRight==-1 && y2!=startres)\r
+ fixedRight = y2 -1;\r
+ if(y1>fixedLeft && fixedLeft==-1)\r
+ fixedLeft = y1;\r
+ }\r
+\r
if (groupEditing)\r
{\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(fixedLeft>sg.getEndRes()\r
- ||fixedRight<sg.getStartRes())\r
- {\r
- endEditing();\r
- return;\r
- }\r
\r
- if (av.hasHiddenRows)\r
+ /*if (av.hasHiddenRows)\r
{\r
//sg might be null as the user may only see 1 sequence\r
if (sg == null)\r
}\r
\r
sg = tmp;\r
- }\r
+ }*/\r
+ // int blankColumn = -1;\r
\r
- if (sg == null)\r
- {\r
- endEditing();\r
- return;\r
- }\r
-\r
- // int blankColumn = -1;\r
\r
// drag to right\r
if (insertGap)\r
{\r
- // Is it valid??\r
+ //If the user has selected the whole sequence, and is dragging to\r
+ // the right, we can still extend the alignment and selectionGroup\r
+ if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())\r
+ {\r
+ sg.setEndRes(av.alignment.getWidth() + startres - lastres);\r
+ fixedRight = sg.getEndRes();\r
+ }\r
+\r
+ // Is it valid with fixed columns??\r
// Find the next gap before the end\r
// of the visible region boundary\r
- if (av.hasHiddenColumns)\r
+ boolean blank = false;\r
+ for (fixedRight = fixedRight;\r
+ fixedRight > lastres;\r
+ fixedRight--)\r
{\r
- // int lastCol = av.getColumnSelection().\r
- // getHiddenRegionBoundary(res);\r
-\r
- }\r
-\r
- if (fixedRight != startres && fixedRight<av.alignment.getWidth()-1)\r
+ blank = true;\r
+ for (int s = 0; s < sg.getSize(); s++)\r
{\r
- for (fixedRight = fixedRight;\r
- fixedRight > lastres;\r
- fixedRight --)\r
+ seq = sg.getSequenceAt(s);\r
+ for (int j = 0; j < startres - lastres; j++)\r
{\r
- boolean blank = true;\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getCharAt(fixedRight - j)))\r
{\r
- seq = sg.getSequenceAt(s);\r
-\r
- if (seq.getSequence().length() <= fixedRight)\r
- {\r
- continue;\r
- }\r
-\r
- if (!jalview.util.Comparison.isGap(\r
- seq.getCharAt(fixedRight)))\r
- {\r
- blank = false;\r
- continue;\r
- }\r
- }\r
- if (blank)\r
+ blank = false;\r
break;\r
+ }\r
}\r
}\r
+ if (blank)\r
+ break;\r
+ }\r
\r
- if (fixedRight <= startres)\r
+ if (!blank)\r
+ {\r
+ if(sg.getSize() == av.alignment.getHeight())\r
+ {\r
+ //We can still insert gaps if the selectionGroup\r
+ //contains all the sequences\r
+ sg.setEndRes(sg.getEndRes()+1+startres-lastres);\r
+ fixedRight = av.alignment.getWidth()+startres-lastres;\r
+ }\r
+ else\r
{\r
endEditing();\r
return;\r
}\r
}\r
+ }\r
\r
\r
// drag to left\r
- else\r
+ else if(!insertGap)\r
{\r
/// Are we able to delete?\r
// ie are all columns blank?\r
}\r
else /////Editing a single sequence///////////\r
{\r
-\r
if (insertGap)\r
{\r
// dragging to the right\r
for (int j = lastres; j < startres; j++)\r
{\r
if (fixedColumns && fixedRight != -1)\r
- insertChar(j, seq, fixedRight);\r
+ {\r
+ if (sg.getStartRes() == 0\r
+ && sg.getEndRes() + 1 == av.alignment.getWidth()\r
+ && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))\r
+ {\r
+ //Single sequence edit, whole sequence selected,\r
+ //extend the selection group\r
+ sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);\r
+ fixedColumns = false;\r
+ insertChar(j, seq);\r
+ }\r
+ else\r
+ insertChar(j, seq, fixedRight);\r
+ }\r
else\r
insertChar(j, seq);\r
}\r
for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
{\r
if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
- {\r
+ {\r
//Theres a space, so break and insert the gap\r
break;\r
}\r
{\r
y = av.alignment.getHeight() -1;\r
}\r
+ if(res> av.alignment.getWidth())\r
+ {\r
+ res = av.alignment.getWidth()-1;\r
+ }\r
\r
if (stretchGroup.getEndRes() == res)\r
{\r
seqCanvas.repaint();\r
}\r
\r
+ void scrollCanvas(MouseEvent evt)\r
+ {\r
+ if(evt==null)\r
+ {\r
+ if(scrollThread!=null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+ mouseDragging = false;\r
+ }\r
+ else\r
+ {\r
+ if (scrollThread == null)\r
+ scrollThread = new ScrollThread();\r
+\r
+ mouseDragging = true;\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ }\r
\r
\r
// this class allows scrolling off the bottom of the visible alignment\r
git://source.jalview.org / jalview.git / commitdiff