+ int fixedLeft = -1;\r
+ int fixedRight = -1;\r
+ boolean fixedColumns = false;\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+\r
+\r
+ if (!groupEditing && av.hasHiddenRows)\r
+ {\r
+ if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
+ {\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
+ SequenceI seq = av.alignment.getSequenceAt(startseq);\r
+ StringBuffer message = new StringBuffer();\r
+ if (groupEditing)\r
+ {\r
+ message.append("Edit group:");\r
+ if (editCommand == null)\r
+ editCommand = new EditCommand("Edit Group");\r
+ }\r
+ else\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
+ else\r
+ message.append(" delete ");\r
+\r
+ message.append(Math.abs(startres-lastres)+" gaps.");\r
+ ap.alignFrame.statusBar.setText(message.toString());\r
+\r
+\r
+ //Are we editing within a selection group?\r
+ if (groupEditing\r
+ || (sg != null && sg.getSequences(true).contains(seq)))\r
+ {\r
+ fixedColumns = true;\r
+\r
+ //sg might be null as the user may only see 1 sequence,\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
+ }\r
+\r
+ fixedLeft = sg.getStartRes();\r
+ fixedRight = sg.getEndRes();\r
+\r
+ if ( (startres < fixedLeft && lastres >= fixedLeft)\r
+ || (startres >= fixedLeft && lastres < fixedLeft)\r
+ || (startres > fixedRight && lastres <=fixedRight)\r
+ || (startres <= fixedRight && lastres > fixedRight))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if (fixedLeft > startres)\r
+ {\r
+ fixedRight = fixedLeft - 1;\r
+ fixedLeft = 0;\r
+ }\r
+ else if (fixedRight < startres)\r
+ {\r
+ fixedLeft = fixedRight;\r
+ fixedRight = -1;\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
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
+ //Selection spans a hidden region\r
+ if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))\r
+ {\r
+ if(startres>=y2)\r
+ {\r
+ fixedLeft = y2;\r
+ }\r
+ else\r
+ {\r
+ fixedRight = y2 - 1;\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ if (groupEditing)\r
+ {\r
+ Vector vseqs = sg.getSequences(true);\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
+ //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\r
+ && sg.getEndRes() == fixedRight\r
+ && sg.getEndRes() == av.alignment.getWidth()-1\r
+ )\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
+ boolean blank = false;\r
+ for (fixedRight = fixedRight;\r
+ fixedRight > lastres;\r
+ fixedRight--)\r
+ {\r
+ blank = true;\r
+\r
+ for (g = 0; g < groupSize; g++)\r
+ {\r
+ for (int j = 0; j < startres - lastres; j++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(\r
+ groupSeqs[g].getCharAt(fixedRight - j)))\r
+ {\r
+ blank = false;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (blank)\r
+ break;\r
+ }\r
+\r
+ if (!blank)\r
+ {\r
+ if(sg.getSize(false) == av.alignment.getHeight() )\r
+ {\r
+ if((av.hasHiddenColumns\r
+ && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ int alWidth = av.alignment.getWidth();\r
+ if(av.hasHiddenRows)\r
+ {\r
+ int hwidth = av.alignment.getHiddenSequences().getWidth();\r
+ if(hwidth>alWidth)\r
+ alWidth = hwidth;\r
+ }\r
+ //We can still insert gaps if the selectionGroup\r
+ //contains all the sequences\r
+ sg.setEndRes(sg.getEndRes()+startres-lastres);\r
+ fixedRight = alWidth+startres-lastres;\r
+ }\r
+ else\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ // drag to left\r
+ else if(!insertGap)\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+\r
+ for (g = 0; g < groupSize; g++)\r
+ {\r
+ for (int j = startres; j < lastres; j++)\r
+ {\r
+ if (groupSeqs[g].getLength() <= j)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(\r
+ groupSeqs[g].getCharAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ insertChar(j, groupSeqs, fixedRight);\r
+ }\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
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j > startres; j--)\r
+ {\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
+ else /////Editing a single sequence///////////\r
+ {\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ insertChar(j, new SequenceI[]{seq}, fixedRight);\r
+ }\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
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
+ {\r
+ endEditing();\r
+ break;\r
+ }\r
+ deleteChar(startres, new SequenceI[]{seq}, fixedRight);\r
+ }\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
+ 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
+ lastres = startres;\r
+ seqCanvas.repaint();\r