\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 jalview.schemes.*;\r
\r
+import java.util.Vector;\r
+\r
public class SeqPanel\r
extends Panel implements MouseMotionListener, MouseListener\r
{\r
\r
protected int lastres;\r
protected int startseq;\r
- int startEdit = -1;\r
- int endEdit = -1;\r
\r
protected AlignViewport av;\r
\r
// if character is inserted or deleted, we will need to recalculate the conservation\r
- int seqEditOccurred = -1;\r
+ boolean seqEditOccurred = false;\r
\r
ScrollThread scrollThread = null;\r
boolean mouseDragging = false;\r
-\r
boolean editingSeqs = false;\r
boolean groupEditing = false;\r
\r
+ int oldSeq = -1;\r
+ boolean changeEndSeq = false;\r
+ boolean changeStartSeq = false;\r
+ boolean changeEndRes = false;\r
+ boolean changeStartRes = false;\r
+ SequenceGroup stretchGroup = null;\r
+\r
+ StringBuffer keyboardNo1;\r
+ StringBuffer keyboardNo2;\r
+\r
+ boolean mouseWheelPressed = false;\r
+ Point lastMousePress;\r
+\r
public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
{\r
this.av = avp;\r
seqCanvas.repaint();\r
}\r
\r
+ void endEditing()\r
+ {\r
+ startseq = -1;\r
+ lastres = -1;\r
+ seqEditOccurred = false;\r
+ editingSeqs = false;\r
+ groupEditing = false;\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
+ 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
+\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
+ if (av.wrapAlignment)\r
+ {\r
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
+ }\r
+ else\r
+ {\r
+ while (seqCanvas.cursorY < av.startSeq)\r
+ {\r
+ ap.scrollUp(true);\r
+ }\r
+ while (seqCanvas.cursorY + 1 > av.endSeq)\r
+ {\r
+ ap.scrollUp(false);\r
+ }\r
+ while (seqCanvas.cursorX < av.startRes)\r
+ {\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
+ void setSelectionAreaAtCursor(boolean topLeft)\r
+ {\r
+ SequenceI sequence =\r
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
+\r
+ if(av.getSelectionGroup()!=null)\r
+ {\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
+ {\r
+ int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
+ if(index > max)\r
+ max = index;\r
+ if(index < min)\r
+ min = index;\r
+ }\r
+\r
+ max ++;\r
+\r
+ if(topLeft)\r
+ {\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+ if(sg.getEndRes()<seqCanvas.cursorX)\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+\r
+ min = seqCanvas.cursorY;\r
+ }\r
+ else\r
+ {\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+ if(sg.getStartRes()>seqCanvas.cursorX)\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+\r
+ max = seqCanvas.cursorY+1;\r
+ }\r
+\r
+ if(min>max)\r
+ {\r
+ // Only the user can do this\r
+ av.setSelectionGroup(null);\r
+ }\r
+ else\r
+ {\r
+ // Now add any sequences between min and max\r
+ sg.getSequences(false).removeAllElements();\r
+ for (int i = min; i < max; i++)\r
+ {\r
+ sg.addSequence(av.alignment.getSequenceAt(i), false);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.getSelectionGroup() == null)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+ sg.addSequence(sequence, false);\r
+ av.setSelectionGroup(sg);\r
+ }\r
+\r
+\r
+ ap.repaint();\r
+ }\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
+ }\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
+ }\r
+\r
+ void numberPressed(char value)\r
+ {\r
+ if(keyboardNo1==null)\r
+ keyboardNo1 = new StringBuffer();\r
+\r
+ if(keyboardNo2!=null)\r
+ keyboardNo2.append(value);\r
+ else\r
+ keyboardNo1.append(value);\r
+ }\r
+\r
+ int getKeyboardNo(StringBuffer kb)\r
+ {\r
+ if(kb==null)\r
+ return 1;\r
+ else\r
+ return Integer.parseInt(kb.toString());\r
+ }\r
+\r
+ void setStatusMessage(SequenceI sequence, int res, int seq)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
+\r
+ Object obj = null;\r
+ if (av.alignment.isNucleotide())\r
+ {\r
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
+ "");\r
+ if (obj != null)\r
+ text.append(" Nucleotide: ");\r
+ }\r
+ else\r
+ {\r
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+ if (obj != null)\r
+ text.append(" Residue: ");\r
+ }\r
+\r
+ if (obj != null)\r
+ {\r
+\r
+ if (obj != "")\r
+ {\r
+ text.append(obj + " (" + sequence.findPosition(res) +\r
+ ")");\r
+ }\r
+ }\r
\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
+ }\r
public void mousePressed(MouseEvent evt)\r
{\r
- if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ lastMousePress = evt.getPoint();\r
+\r
+ if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==\r
+ InputEvent.BUTTON2_MASK)\r
+ {\r
+ mouseWheelPressed = true;\r
+ return;\r
+ }\r
+\r
+ if (evt.isShiftDown() || evt.isAltDown() ||\r
+ 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
+ return;\r
}\r
+\r
+\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\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
+ {\r
+ startseq = seq;\r
+ lastres = res;\r
+ }\r
+ else\r
+ {\r
+ startseq = -1;\r
+ lastres = -1;\r
+ }\r
+\r
+ return;\r
}\r
\r
public void mouseClicked(MouseEvent evt){}\r
\r
public void mouseReleased(MouseEvent evt)\r
{\r
+ mouseDragging = false;\r
+ mouseWheelPressed = false;\r
+\r
if (!editingSeqs)\r
{\r
- doMouseReleasedDefineMode(evt);\r
- return;\r
+ doMouseReleasedDefineMode(evt);\r
+ return;\r
}\r
\r
+ editOccurred();\r
\r
- if (seqEditOccurred > -1)\r
- {\r
- editOccurred(seqEditOccurred);\r
- }\r
-\r
- startseq = -1;\r
- lastres = -1;\r
- seqEditOccurred = -1;\r
- editingSeqs = false;\r
- groupEditing = false;\r
- ap.repaint();\r
+ endEditing();\r
+ ap.repaint();\r
}\r
\r
int startWrapBlock=-1;\r
&& sequence.getSequenceFeatures()!=null\r
&& av.featuresDisplayed!=null)\r
{\r
+ StringBuffer featureText = new StringBuffer();\r
+ Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));\r
+\r
int index = 0;\r
- sequence.getSequenceFeatures();\r
- boolean first = true;\r
- while (index < sequence.getSequenceFeatures().length)\r
+ while (index < allFeatures.size())\r
{\r
- SequenceFeature sf = sequence.getSequenceFeatures()[index];\r
- if (sf.getBegin() <= sequence.findPosition(res) &&\r
- sf.getEnd() >= sequence.findPosition(res))\r
- {\r
- if(!av.featuresDisplayed.containsKey(sf.getType()))\r
- {\r
- index++;\r
- continue;\r
- }\r
-\r
- if(first)\r
- {\r
- text.append(" Sequence Feature:");\r
- first = false;\r
- }\r
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);\r
\r
- text.append(" "+sf.getType());\r
+ featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);\r
\r
- if(sf.getDescription()!=null)\r
- text.append(" "+sf.getDescription());\r
+ if (sf.getDescription() != null)\r
+ featureText.append(" " + sf.getDescription());\r
\r
- if (sf.getStatus()!=null && sf.getStatus().length() > 0)\r
- {\r
- text.append(" (" + sf.getStatus() + ")");\r
- }\r
- text.append("; ");\r
+ if (sf.getValue("status") != null )\r
+ {\r
+ featureText.append(" (" + sf.getValue("status") + ")");\r
}\r
+ featureText.append("\n");\r
\r
index++;\r
-\r
}\r
+\r
+\r
+ if (tooltip == null)\r
+ tooltip = new Tooltip(featureText.toString(), seqCanvas);\r
+ else\r
+ tooltip.setTip(featureText.toString());\r
+\r
+ tooltip.repaint();\r
+\r
+ // text.append(" Sequence Feature:");\r
+ // text.append(featureText);\r
+\r
}\r
\r
+\r
ap.alignFrame.statusBar.setText(text.toString());\r
\r
}\r
\r
- public void mouseDragged(MouseEvent evt)\r
+ Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
{\r
- if (!editingSeqs)\r
+ Vector allFeatures = new Vector();\r
+ int index = 0;\r
+ if(seq.getSequenceFeatures()!=null)\r
{\r
- doMouseDraggedDefineMode(evt);\r
- return;\r
+ while (index < seq.getSequenceFeatures().length)\r
+ {\r
+ SequenceFeature sf = seq.getSequenceFeatures()[index];\r
+ if (sf.getBegin() <= res &&\r
+ sf.getEnd() >= res)\r
+ {\r
+ if (av.featuresDisplayed.containsKey(sf.getType()))\r
+ {\r
+ allFeatures.addElement(sf);\r
+ }\r
+ }\r
+ index++;\r
+ }\r
}\r
+ return allFeatures;\r
+ }\r
\r
- // If we're dragging we're editing\r
- int res = findRes(evt);\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
+ Tooltip tooltip;\r
\r
- if (lastres == -1 || lastres == res)\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (mouseWheelPressed)\r
{\r
- return;\r
- }\r
+ int oldWidth = av.charWidth;\r
\r
- boolean dragRight = true;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- dragRight = false;\r
- }\r
+ //Which is bigger, left-right or up-down?\r
+ if (Math.abs(evt.getY() - lastMousePress.y)\r
+ > Math.abs(evt.getX() - lastMousePress.x))\r
+ {\r
+ int fontSize = av.font.getSize();\r
\r
- if (res != lastres)\r
- {\r
- // Group editing\r
- if (groupEditing)\r
+ if (evt.getY() < lastMousePress.y && av.charHeight > 1)\r
+ {\r
+ fontSize--;\r
+ }\r
+ else if (evt.getY() > lastMousePress.y)\r
+ {\r
+ fontSize++;\r
+ }\r
+\r
+\r
+ if(fontSize<1)\r
+ fontSize = 1;\r
+\r
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
+ av.charWidth = oldWidth;\r
+ }\r
+ else\r
{\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if (sg == null)\r
+ if (evt.getX() < lastMousePress.x && av.charWidth > 1)\r
{\r
- lastres = -1;\r
- return;\r
+ av.charWidth--;\r
+ }\r
+ else if (evt.getX() > lastMousePress.x)\r
+ {\r
+ av.charWidth++;\r
}\r
\r
- // drag to right\r
- if (dragRight)\r
+ if(av.charWidth<1)\r
{\r
- sg.setEndRes(sg.getEndRes() + (res - lastres));\r
+ av.charWidth = 1;\r
}\r
+ }\r
+\r
+ ap.fontChanged();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;\r
+\r
+ lastMousePress = evt.getPoint();\r
+\r
+ ap.repaint();\r
+ ap.annotationPanel.image = null;\r
+ return;\r
+ }\r
+\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseDraggedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
+ int res = findRes(evt);\r
+\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
\r
- // drag to left\r
+ if ((lastres == -1) || (lastres == res))\r
+ {\r
+ return;\r
+ }\r
+\r
+ if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
+ {\r
+ // dragLeft, delete gap\r
+ editSequence(false, res);\r
+ }\r
+ else\r
+ editSequence(true, res);\r
+\r
+ mouseDragging = true;\r
+ if(scrollThread!=null)\r
+ scrollThread.setEvent(evt);\r
+\r
+ }\r
+\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(groupEditing && sg==null)\r
+ return;\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 sequence: "+seq.getName());\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(false).contains(seq)))\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
- continue;\r
- }\r
+ fixedColumns = true;\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
+ fixedLeft = sg.getStartRes();\r
+ fixedRight = sg.getEndRes();\r
\r
- if (!deleteAllowed)\r
+ if ( (startres < fixedLeft && lastres >= fixedLeft)\r
+ || (startres >= fixedLeft && lastres < fixedLeft)\r
+ || (startres > fixedRight && lastres <=fixedRight)\r
+ || (startres <= fixedRight && lastres > fixedRight))\r
{\r
- lastres = -1;\r
+ endEditing();\r
return;\r
}\r
\r
- sg.setEndRes(sg.getEndRes() - (lastres - res));\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
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
\r
+ if (groupEditing)\r
+ {\r
// drag to right\r
- if (dragRight)\r
+ if (insertGap)\r
{\r
- for (int j = lastres; j < res; j++)\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
+ boolean blank = false;\r
+ for (fixedRight = fixedRight;\r
+ fixedRight > lastres;\r
+ fixedRight--)\r
{\r
- insertChar(j, k);\r
+ blank = true;\r
+ for (int s = 0; s < sg.getSize(false); s++)\r
+ {\r
+ seq = sg.getSequenceAt(s);\r
+ for (int j = 0; j < startres - lastres; j++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.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
+ //We can still insert gaps if the selectionGroup\r
+ //contains all the sequences\r
+ sg.setEndRes(sg.getEndRes()+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
- for (int j = res; j < lastres; j++)\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+\r
+ for (int s = 0; s < sg.getSize(false); s++)\r
{\r
- if (s.getLength() > j)\r
+ seq = sg.getSequenceAt(s);\r
+\r
+ for (int j = startres; j < lastres; j++)\r
{\r
- deleteChar(res, k);\r
+ if (seq.getSequence().length() <= j)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getSequence().charAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ endEditing();\r
+ return;\r
+ }\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
+\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
- insertChar(j, startseq);\r
+ seq = sg.getSequenceAt(i);\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
+ {\r
+ insertChar(j, seq, fixedRight);\r
+ }\r
+ else\r
+ insertChar(j, seq);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ deleteChar(startres, seq, fixedRight);\r
+ }\r
+ else\r
+ {\r
+ deleteChar(startres, seq);\r
+ }\r
+ }\r
+ }\r
}\r
}\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\r
+ else /////Editing a single sequence///////////\r
{\r
- // dragging to the left\r
- for (int j = lastres; j > res; j--)\r
+ if (insertGap)\r
{\r
- if (jalview.util.Comparison.isGap(\r
- av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
+ // dragging to the right\r
+ for (int j = lastres; j < startres; j++)\r
{\r
-\r
- deleteChar(res, startseq);\r
+ if (fixedColumns && fixedRight != -1)\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
- else\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
{\r
- if(scrollThread!=null)\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ deleteChar(startres, seq, fixedRight);\r
+ }\r
+ else\r
{\r
- scrollThread.running = false;\r
- scrollThread = null;\r
+ deleteChar(startres, seq);\r
}\r
- break;\r
}\r
}\r
}\r
\r
- }\r
+ lastres = startres;\r
+ seqCanvas.repaint();\r
}\r
\r
- mouseDragging = true;\r
- if (res > av.endRes || res < av.startRes)\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
- mouseExited(evt);\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
}\r
\r
- if (scrollThread != null)\r
- scrollThread.setEvent(evt);\r
+ void insertChar(int j, SequenceI seq, int fixedColumn)\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
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
+ {\r
+ //Theres a space, so break and insert the gap\r
+ break;\r
+ }\r
+ }\r
\r
+ if (blankColumn <= j)\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
\r
- endEdit = res;\r
- lastres = res;\r
- seqCanvas.repaint();\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
- public void insertChar(int j, int seq)\r
- {\r
- av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = seq;\r
- }\r
+ seq.deleteCharAt(blankColumn);\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
\r
- public void deleteChar(int j, int seq)\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
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
- seqEditOccurred = seq;\r
- av.alignment.getWidth();\r
- repaint();\r
- }\r
+ seq.deleteCharAt(j);\r
+ seq.insertCharAt(fixedColumn, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
\r
- void editOccurred(int i)\r
- {\r
- if (endEdit == startEdit)\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
+\r
+ seq.deleteCharAt(j);\r
+ seqEditOccurred = true;\r
+ seqCanvas.repaint();\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
+ }\r
\r
- av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
- }\r
+ endEditing();\r
+\r
+ av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
+\r
+ }\r
\r
//////////////////////////////////////////\r
/////Everything below this is for defining the boundary of the rubberband\r
//////////////////////////////////////////\r
- int oldSeq = -1;\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.sequences.contains(sequence)\r
+ else if (!stretchGroup.getSequences(false).contains(sequence)\r
|| stretchGroup.getStartRes() > res\r
|| stretchGroup.getEndRes() < res)\r
{\r
allGroups[i].getEndRes() >= res)\r
{\r
stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
break;\r
}\r
}\r
}\r
+ av.setSelectionGroup(stretchGroup);\r
}\r
\r
- if (stretchGroup == null)\r
+ if (av.cursorMode)\r
{\r
- // define a new group here\r
- SequenceGroup sg = new SequenceGroup();\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
- sg.addSequence(sequence, false);\r
- av.setSelectionGroup(sg);\r
- stretchGroup = sg;\r
+ seqCanvas.cursorX = findRes(evt);\r
+ seqCanvas.cursorY = findSeq(evt);\r
+ seqCanvas.repaint();\r
+ return;\r
+ }\r
\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) ==\r
+ if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
InputEvent.BUTTON3_MASK)\r
{\r
- APopupMenu popup = new APopupMenu(ap, null, null);\r
+ Vector allFeatures = getAllFeaturesAtRes(sequence,\r
+ sequence.findPosition(res));\r
+\r
+ Vector links = null;\r
+ if(allFeatures!=null)\r
+ {\r
+ for (int i = 0; i < allFeatures.size(); i++)\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
+ if (sf.links != null)\r
+ {\r
+ links = new Vector();\r
+ for (int j = 0; j < sf.links.size(); j++)\r
+ {\r
+ links.addElement(sf.links.elementAt(j));\r
+ }\r
+ }\r
+ }\r
+ }\r
+ APopupMenu popup = new APopupMenu(ap, null, links);\r
this.add(popup);\r
popup.show(this, evt.getX(), evt.getY());\r
+ ap.repaint();\r
}\r
-\r
- if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
+ else\r
{\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
- }\r
+ //Only if left mouse button do we want to change group sizes\r
\r
- else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeStartRes = true;\r
- }\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, false);\r
+ av.setSelectionGroup(sg);\r
+ stretchGroup = sg;\r
+\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
\r
- boolean changeEndSeq = false;\r
- boolean changeStartSeq = false;\r
- boolean changeEndRes = false;\r
- boolean changeStartRes = false;\r
- SequenceGroup stretchGroup = null;\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
+ {\r
+ // Edit end res position of selected group\r
+ changeStartRes = true;\r
+ }\r
+ }\r
+ }\r
\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
{\r
if (stretchGroup.cs instanceof ClustalxColourScheme)\r
{\r
- ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
- sequences,\r
+ ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
+ stretchGroup.getSequences(true),\r
stretchGroup.getWidth());\r
}\r
\r
\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
- if (stretchGroup.sequences.contains(nextSeq))\r
+ if (stretchGroup.getSequences(false).contains(nextSeq))\r
{\r
stretchGroup.deleteSequence(seq, false);\r
}\r
git://source.jalview.org / jalview.git / blobdiff