X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=9b2f5f43d67646e14a4404d24acd1213028823ee;hb=94bc21544b9573fdf177c500bdb981e8076a7e7d;hp=b48861a0d34130ece6a660e774363376a6d994bf;hpb=2ece3719ca3be664ef49768ff8334d1f257720f3;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index b48861a..9b2f5f4 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,675 +1,1429 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; +import jalview.datamodel.*; + +import jalview.schemes.*; + import java.awt.*; import java.awt.event.*; -import jalview.datamodel.*; + import javax.swing.*; -import java.util.*; -import jalview.schemes.*; -import jalview.analysis.Conservation; -public class SeqPanel extends JPanel + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqPanel extends JPanel implements MouseListener, + MouseMotionListener, MouseWheelListener + { + /** DOCUMENT ME!! */ + public SeqCanvas seqCanvas; + + /** DOCUMENT ME!! */ + public AlignmentPanel ap; + protected int lastres; + protected int startseq; + protected AlignViewport av; + + // if character is inserted or deleted, we will need to recalculate the conservation + boolean seqEditOccurred = false; + ScrollThread scrollThread = null; + boolean mouseDragging = false; + boolean editingSeqs = false; + boolean groupEditing = false; + + ////////////////////////////////////////// + /////Everything below this is for defining the boundary of the rubberband + ////////////////////////////////////////// + int oldSeq = -1; + boolean changeEndSeq = false; + boolean changeStartSeq = false; + boolean changeEndRes = false; + boolean changeStartRes = false; + SequenceGroup stretchGroup = null; + boolean remove = false; + + boolean mouseWheelPressed = false; + StringBuffer keyboardNo1; + StringBuffer keyboardNo2; + + /** + * Creates a new SeqPanel object. + * + * @param avp DOCUMENT ME! + * @param p DOCUMENT ME! + */ + public SeqPanel(AlignViewport avp, AlignmentPanel p) + { + ToolTipManager.sharedInstance().registerComponent(this); + ToolTipManager.sharedInstance().setInitialDelay(0); + ToolTipManager.sharedInstance().setDismissDelay(10000); + this.av = avp; + setBackground(Color.white); + + seqCanvas = new SeqCanvas(avp); + setLayout(new BorderLayout()); + add(seqCanvas, BorderLayout.CENTER); + + ap = p; - public SeqCanvas seqCanvas; - public AlignmentPanel ap; + if(!av.isDataset()) + { + addMouseMotionListener(this); + addMouseListener(this); + addMouseWheelListener(this); + } + } - protected int lastres; - protected int startseq; - int startEdit=-1; - int endEdit=-1; + int startWrapBlock=-1; + int wrappedBlock=-1; + int findRes(MouseEvent evt) + { + int res = 0; + int x = evt.getX(); - protected AlignViewport av; + if (av.wrapAlignment) + { - // if character is inserted or deleted, we will need to recalculate the conservation - int seqEditOccurred = -1; + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - ScrollThread scrollThread = null; - boolean mouseDragging = false; + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); - boolean editingSeqs = false; - boolean groupEditing = false; + int y = evt.getY(); + y -= hgap; + x -= seqCanvas.LABEL_WEST; - public SeqPanel(AlignViewport avp, AlignmentPanel p) { - this.av = avp; + int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); - seqCanvas = new SeqCanvas(avp); - setLayout(new BorderLayout()); - add(seqCanvas, BorderLayout.CENTER); + wrappedBlock = y / cHeight; + wrappedBlock += av.getStartRes() / cwidth; - ap = p; + res = wrappedBlock * cwidth + x / av.getCharWidth(); - addMouseMotionListener( new MouseMotionAdapter() + } + else { - public void mouseMoved(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - doMouseMoved(evt); } + res = (x / av.getCharWidth()) + av.getStartRes(); + } + + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + + return res; + + } + + int findSeq(MouseEvent evt) + { + + int seq = 0; + int y = evt.getY(); + + if (av.wrapAlignment) + { + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; + + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); + + y -= hgap; - public void mouseDragged(MouseEvent evt) + seq = ( (y % cHeight) / av.getCharHeight()); + } + else + { + seq = (y / av.getCharHeight()) + av.getStartSeq(); + } + + return seq; + } + + void endEditing() + { + startseq = -1; + lastres = -1; + seqEditOccurred = false; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + } + + void setCursorRow() + { + seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorRowAndColumn() + { + if(keyboardNo2==null) { - if(av.getWrapAlignment()) - return; - if( editingSeqs ) - doMouseDragged(evt); - else - doMouseDraggedDefineMode(evt); + keyboardNo2 = new StringBuffer(); } - }); + else + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; + seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; + scrollToVisible(); + } + } - addMouseListener( new MouseAdapter() + void setCursorPosition() { - public void mouseReleased(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - if(editingSeqs) - doMouseReleased(evt); - else - doMouseReleasedDefineMode(evt); + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + + seqCanvas.cursorX = sequence.findIndex( + getKeyboardNo(keyboardNo1)-1 + ); + scrollToVisible(); + } + + void moveCursor(int dx, int dy) + { + seqCanvas.cursorX += dx; + seqCanvas.cursorY += dy; + scrollToVisible(); + } + + void scrollToVisible() + { + if (seqCanvas.cursorX < 0) + seqCanvas.cursorX = 0; + else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) + seqCanvas.cursorX = av.alignment.getWidth() - 1; + + if (seqCanvas.cursorY < 0) + seqCanvas.cursorY = 0; + else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + seqCanvas.cursorY = av.alignment.getHeight() - 1; + + endEditing(); + while (seqCanvas.cursorY < av.startSeq) + { + ap.scrollUp(true); } - public void mousePressed(MouseEvent evt) + while (seqCanvas.cursorY + 1 > av.endSeq) { - if(av.getWrapAlignment()) - return; - if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) - { - if(evt.isAltDown() || evt.isControlDown()) - groupEditing = true; - - editingSeqs = true; - doMousePressed(evt); - } - else - doMousePressedDefineMode(evt); + ap.scrollUp(false); } - public void mouseExited(MouseEvent evt) + while (seqCanvas.cursorX < av.startRes) { - if (av.getWrapAlignment() || editingSeqs) - return; - doMouseExitedDefineMode(evt); - + if(!ap.scrollRight(false)) + break; } - public void mouseEntered(MouseEvent evt) + while (seqCanvas.cursorX > av.endRes) { - if (av.getWrapAlignment() || editingSeqs) - return; - doMouseEnteredDefineMode(evt); + if(!ap.scrollRight(true)) + break; } - }); - repaint(); - } + setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + seqCanvas.cursorX, seqCanvas.cursorY); + seqCanvas.repaint(); + } - public void doMouseReleased(MouseEvent evt) { + void setSelectionAreaAtCursor(boolean topLeft) + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); - if(seqEditOccurred>-1) - editOccurred(seqEditOccurred); + if(av.getSelectionGroup()!=null) + { + SequenceGroup sg = av.selectionGroup; + //Find the top and bottom of this group + int min = av.alignment.getHeight(), max = 0; + for(int i=0; i max) + max = index; + if(index < min) + min = index; + } - startseq = -1; - lastres = -1; - seqEditOccurred = -1; - editingSeqs = false; - groupEditing = false; + max ++; - ap.repaint(); - } + if(topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if(sg.getEndRes()seqCanvas.cursorX) + sg.setStartRes(seqCanvas.cursorX); - ap.alignFrame.addHistoryItem( new HistoryItem( - "Edit Sequence",av.alignment, HistoryItem.EDIT)); + max = seqCanvas.cursorY+1; + } - int seq; - int res; + if(min>max) + { + // Only the user can do this + av.setSelectionGroup(null); + } + else + { + // Now add any sequences between min and max + sg.sequences.clear(); + for (int i = min; i < max; i++) + { + sg.addSequence(av.alignment.getSequenceAt(i), false); + } + } + } + + if (av.getSelectionGroup() == null) + { + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(seqCanvas.cursorX); + sg.setEndRes(seqCanvas.cursorX); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + } - int x = evt.getX(); - int y = evt.getY(); - res = x/av.getCharWidth() + av.getStartRes(); - seq = y/av.getCharHeight() + av.getStartSeq(); + ap.repaint(); + } - if (seq < av.getAlignment().getHeight() && - res < av.getAlignment().getSequenceAt(seq).getLength()) + void insertGapAtCursor(boolean group) { - startseq = seq; - lastres = res; + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); + editOccurred(); } - else + + void deleteGapAtCursor(boolean group) { - startseq = -1; - lastres = -1; + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); + editSequence(false, seqCanvas.cursorX); + editOccurred(); } - startEdit = lastres; - endEdit = lastres; + void numberPressed(char value) + { + if(keyboardNo1==null) + keyboardNo1 = new StringBuffer(); - return; - } + if(keyboardNo2!=null) + keyboardNo2.append(value); + else + keyboardNo1.append(value); + } - public void doMouseMoved(MouseEvent evt) - { - int res=0, seq=0; - int x = evt.getX(); - int y = evt.getY(); - if(av.wrapAlignment) + int getKeyboardNo(StringBuffer kb) { - y -= 2*av.charHeight; - int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight; + if(kb==null) + return 1; + else + return Integer.parseInt(kb.toString()); + } - res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes(); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseReleased(MouseEvent evt) + { + mouseDragging = false; + mouseWheelPressed = false; + + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } - y %= chunkHeight; - seq = y / av.getCharHeight() + av.getStartSeq(); + editOccurred(); + endEditing(); + ap.repaint(); } - else + + + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mousePressed(MouseEvent evt) { - res = x / av.getCharWidth() + av.getStartRes(); - seq = y / av.getCharHeight() + av.getStartSeq(); - } + if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + { + mouseWheelPressed = true; + return; + } + if (evt.isShiftDown() || evt.isAltDown() || + evt.isControlDown()) + { + if (evt.isAltDown() || evt.isControlDown()) + { + groupEditing = true; + } + editingSeqs = true; + } + else + { + doMousePressedDefineMode(evt); + return; + } - if(seq>=av.getAlignment().getHeight()) - return; - SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if(res>sequence.getLength()) - return; - Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ; - String aa = ""; - if(obj!=null) - aa = obj.toString(); + int seq = findSeq(evt); + int res = findRes(evt); - StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName()); - if(aa!="") - text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")"); + if(seq<0 || res<0) + return; - ap.alignFrame.statusBar.setText(text.toString()); + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); - // use aa to see if the mouse pointer is on a - if( av.showSequenceFeatures) + if ((seq < av.getAlignment().getHeight()) && + (res < av.getAlignment().getSequenceAt(seq).getLength())) + { + startseq = seq; + lastres = res; + } + else + { + startseq = -1; + lastres = -1; + } + + return; + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseMoved(MouseEvent evt) { - Vector features = sequence.getSequenceFeatures(); - Enumeration e = features.elements(); - StringBuffer sbuffer = new StringBuffer(); + if (editingSeqs) + { + // This is because MacOSX creates a mouseMoved + // If control is down, other platforms will not. + mouseDragged(evt); + } + + int res = findRes(evt); + int seq = findSeq(evt); + + + if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) + return; + + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + if (res > sequence.getLength()) + { + return; + } - while (e.hasMoreElements()) + if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) { - SequenceFeature sf = (SequenceFeature) e.nextElement(); - if (sf.getStart() <= sequence.findPosition(res) && - sf.getEnd() >= sequence.findPosition(res)) + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + } + + setStatusMessage(sequence, res, seq); + + // use aa to see if the mouse pointer is on a + if (av.showSequenceFeatures) { - if(sbuffer.length()>0) - sbuffer.append("; "); - sbuffer.append(sf.getType() + " " + sf.getDescription()); - if(sf.getStatus().length()>0) - sbuffer.append(" ("+sf.getStatus()+")"); + SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); + if(features!=null) + { + StringBuffer sbuffer = new StringBuffer(""); + + for (int i = 0; i < features.length; i++) + { + + if ( (features[i].getBegin() <= sequence.findPosition(res)) && + (features[i].getEnd() >= sequence.findPosition(res))) + { + if(av.featuresDisplayed==null + || !av.featuresDisplayed.containsKey(features[i].getType())) + continue; + + + if (features[i].getType().equals("disulfide bond")) + { + if (features[i].getBegin() == sequence.findPosition(res) + || features[i].getEnd() == sequence.findPosition(res)) + { + if (sbuffer.length() > 6) + sbuffer.append("
"); + sbuffer.append("disulfide bond " + features[i].getBegin() + ":" + + features[i].getEnd()); + } + } + else + { + if (sbuffer.length() > 6) + sbuffer.append("
"); + if(features[i].featureGroup!=null) + sbuffer.append(features[i].featureGroup+";"); + + sbuffer.append(features[i].getType()); + + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) + sbuffer.append("; " + features[i].getDescription()); + + if (features[i].getStatus() != null && features[i].getStatus().length()>0) + { + sbuffer.append("; (" + features[i].getStatus() + ")"); + } + } + } + + } + + sbuffer.append(""); + if(sbuffer.length()==13) // + setToolTipText(""); + else + setToolTipText(sbuffer.toString()); + } + else + setToolTipText(""); } + } + void setStatusMessage(SequenceI sequence, int res, int seq) + { + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); + + Object obj = null; + if (av.alignment.isNucleotide()) + { + obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + + ""); + if (obj != null) + text.append(" Nucleotide: "); } + else + { + obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + if (obj != null) + text.append(" Residue: "); + } + + if (obj != null) + { + + if (obj != "") + { + text.append(obj + " (" + sequence.findPosition(res) + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); - ToolTipManager.sharedInstance().registerComponent(this); - this.setToolTipText(sbuffer.toString()); } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseDragged(MouseEvent evt) + { + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } - } + int res = findRes(evt); - public void doMouseDragged(MouseEvent evt) { + if (res < 0) + { + res = 0; + } - // If we're dragging we're editing - int res = evt.getX() / av.getCharWidth() + av.getStartRes(); - if (res < 0) - res = 0; + if ((lastres == -1) || (lastres == res)) + { + return; + } - if (lastres == -1 || lastres == res) - return; + if ( (res < av.getAlignment().getWidth()) && (res < lastres)) + { + // dragLeft, delete gap + editSequence(false, res); + } + else + editSequence(true, res); - boolean dragRight = true; - if (res < av.getAlignment().getWidth() && res < lastres) - dragRight = false; + mouseDragging = true; + if(scrollThread!=null) + scrollThread.setEvent(evt); + } - if (res != lastres) + synchronized void editSequence(boolean insertGap, int startres) { - // Group editing + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); + + if(groupEditing && sg==null) + return; + + if (!groupEditing && av.hasHiddenRows) + { + //This needs to check all the sequences in a group edit,m + // not just the startseq + if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) + { + groupEditing = true; + } + } + + SequenceI seq = av.alignment.getSequenceAt(startseq); + StringBuffer message = new StringBuffer(); if (groupEditing) + message.append("Edit group:"); + else + message.append("Edit sequence: "+seq.getName()); + + if(insertGap) + message.append(" insert "); + else + message.append(" delete "); + + message.append(Math.abs(startres-lastres)+" gaps."); + ap.alignFrame.statusBar.setText(message.toString()); + + + //Are we editing within a selection group? + if (groupEditing + || (sg != null && sg.sequences.contains(seq))) { - SequenceGroup sg = av.getSelectionGroup(); - if(sg==null) + fixedColumns = true; + + fixedLeft = sg.getStartRes(); + fixedRight = sg.getEndRes(); + + if ( (startres < fixedLeft && lastres >= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <=fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) { - lastres=-1; + endEditing(); return; } - // drag to right - if(dragRight) - sg.setEndRes(sg.getEndRes() + (res-lastres)); + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } + } - // drag to left - else + + + if(av.hasHiddenColumns) + { + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + + if( ( insertGap && startres>y1 && lastresy2) ) + { + endEditing(); + return; + } + + if(fixedRightfixedLeft && fixedLeft==-1) + fixedLeft = y1; + } + + if (groupEditing) + { + + /*if (av.hasHiddenRows) + { + //sg might be null as the user may only see 1 sequence + if (sg == null) { - /// Are we able to delete? - // ie are all columns blank? - boolean deleteAllowed = false; + sg = new SequenceGroup(); + sg.addSequence(av.alignment.getSequenceAt(startseq), false); + } + + SequenceGroup tmp = new SequenceGroup(); + + //Do any of the sequences have hidden associates? + for (int s = 0; s < sg.getSize(); s++) + { + seq = sg.getSequenceAt(s); + tmp.addSequence(seq, false); + if (seq.getHiddenSequences() != null) + { + for (int h = 0; h < seq.getHiddenSequences().getSize(); h++) + tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h), + false); + } + } + + sg = tmp; + }*/ + // int blankColumn = -1; + + + // drag to right + if (insertGap) + { + //If the user has selected the whole sequence, and is dragging to + // the right, we can still extend the alignment and selectionGroup + if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth()) + { + sg.setEndRes(av.alignment.getWidth() + startres - lastres); + fixedRight = sg.getEndRes(); + } + + // Is it valid with fixed columns?? + // Find the next gap before the end + // of the visible region boundary + boolean blank = false; + for (fixedRight = fixedRight; + fixedRight > lastres; + fixedRight--) + { + blank = true; for (int s = 0; s < sg.getSize(); s++) { - SequenceI seq = sg.getSequenceAt(s); - for (int j=res; jj) - deleteChar(res, k); + insertChar(j, seq, fixedRight); } + else + insertChar(j, seq); } } + else + { + // dragging to the left + for (int j = lastres; j > startres; j--) + { + if (fixedColumns && fixedRight != -1) + { + deleteChar(startres, seq, fixedRight); + } + else + { + deleteChar(startres, seq); + } + } + } + } } else /////Editing a single sequence/////////// { - if (res < av.getAlignment().getWidth() && res > lastres) + if (insertGap) { // dragging to the right - for (int j = lastres; j < res; j++) - insertChar(j, startseq); + for (int j = lastres; j < startres; j++) + { + if (fixedColumns && fixedRight != -1) + { + if (sg.getStartRes() == 0 + && sg.getEndRes() + 1 == av.alignment.getWidth() + && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight))) + { + //Single sequence edit, whole sequence selected, + //extend the selection group + sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres); + fixedColumns = false; + insertChar(j, seq); + } + else + insertChar(j, seq, fixedRight); + } + else + insertChar(j, seq); + } } - else if (res < av.getAlignment().getWidth() && res < lastres) + else { // dragging to the left - for (int j = lastres; j > res; j--) + for (int j = lastres; j > startres; j--) { - if( jalview.util.Comparison.isGap( - av.alignment.getSequenceAt(startseq).getSequence().charAt(res))) - - deleteChar(res, startseq); + if (fixedColumns && fixedRight != -1) + { + deleteChar(startres, seq, fixedRight); + } else { - - break; + deleteChar(startres, seq); } } } - } + + lastres = startres; + seqCanvas.repaint(); } - endEdit = res; - lastres = res; - repaint(); - } - public void drawChars(int seqstart, int seqend, int start) { - seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0); - repaint(); - } + /** + * DOCUMENT ME! + * + * @param j DOCUMENT ME! + * @param seq DOCUMENT ME! + */ + void insertChar(int j, SequenceI seq) + { + seq.insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = true; + } - public void insertChar(int j, int seq) - { - av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred=seq; - } + void insertChar(int j, SequenceI seq, int fixedColumn) + { + //Find the next gap before the end of the visible region boundary + //If lastCol > j, theres a boundary after the gap insertion + int blankColumn = fixedColumn; + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } + } - public void deleteChar(int j, int seq) - { - av.alignment.getSequenceAt(seq).deleteCharAt(j); - seqEditOccurred=seq; + if (blankColumn <= j) + { + endEditing(); + return; + } - av.alignment.getWidth(); - repaint(); - } + if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + { + //Just Checking + System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn)); + return; + } + seq.deleteCharAt(blankColumn); + seq.insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = true; + } - void editOccurred(int i) - { - if(endEdit==startEdit) + void deleteChar(int j, SequenceI seq, int fixedColumn) { - ap.alignFrame.historyList.pop(); - ap.alignFrame.updateEditMenuBar(); + if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + { + ap.alignFrame.statusBar.setText( + "End editing: Tried removing residue " + seq.getCharAt(j)); + return; + } + + seq.deleteCharAt(j); + seq.insertCharAt(fixedColumn, av.getGapCharacter()); + seqEditOccurred = true; } - av.updateConservation(); - av.updateConsensus(); + /** + * DOCUMENT ME! + * + * @param j DOCUMENT ME! + * @param seq DOCUMENT ME! + */ + void deleteChar(int j, SequenceI seq) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + { + ap.alignFrame.statusBar.setText( + "End editing: Tried removing residue " + seq.getCharAt(j)); + return; + } - // Y O Y CLUSTALX - ColourSchemeI cs = av.getGlobalColourScheme(); - if(cs instanceof ConservationColourScheme) + seq.deleteCharAt(j); + seqEditOccurred = true; + seqCanvas.repaint(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) { - ConservationColourScheme ccs = (ConservationColourScheme) cs; - if(ccs.cs instanceof ClustalxColourScheme) - { - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - av.alignment.getSequences(), 0, - av.alignment.getWidth() - 1); - c.calculate(); - c.verdict(false, av.ConsPercGaps); - - ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs; - cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth()); - ccs = new ConservationColourScheme(c, cxs); - av.setGlobalColourScheme(ccs); - } + if(oldSeq < 0) + oldSeq = 0; + + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } } - if(cs instanceof ClustalxColourScheme) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) { - ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(), - av.alignment.getWidth()); - av.setGlobalColourScheme(cs); + if (av.getWrapAlignment()) + { + return; + } + + if (mouseDragging) + { + scrollThread = new ScrollThread(); + } } - } + public void mouseClicked(MouseEvent evt) + {} -////////////////////////////////////////// -/////Everything below this is for defining the boundary of the rubberband -////////////////////////////////////////// - int oldSeq = -1; - public void doMousePressedDefineMode(MouseEvent evt) - { - int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - int seq = evt.getY()/av.getCharHeight() + av.getStartSeq(); - oldSeq = seq; + public void mouseWheelMoved(MouseWheelEvent e) + { + e.consume(); + if (mouseWheelPressed) + { + Font font = av.getFont(); + int fontSize = font.getSize(); + if (e.getWheelRotation() > 0 && fontSize < 51) + fontSize++; + else if (fontSize > 1) + fontSize--; + + av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); + ap.fontChanged(); + } + else + { + if (e.getWheelRotation() > 0) + ap.scrollUp(false); + else + ap.scrollUp(true); + } - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); + } - if(sequence==null || res>sequence.getLength()) - return; - stretchGroup = av.getSelectionGroup(); - if(stretchGroup == null) - { - stretchGroup = av.alignment.findGroup( sequence ); - if(stretchGroup!=null && res>stretchGroup.getStartRes() && resres - || stretchGroup.getEndRes()= res) - { - stretchGroup = allGroups[i]; - av.setSelectionGroup(stretchGroup); - break; - } - } - - if(stretchGroup==null) + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + */ + void editOccurred() { - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence( sequence ); - av.setSelectionGroup( sg ); - stretchGroup = sg; + if (!seqEditOccurred) + { + ap.alignFrame.historyList.pop(); + ap.alignFrame.updateEditMenuBar(); + } - if(av.getConservationSelected()) - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background"); - if(av.getAbovePIDThreshold()) - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background"); + endEditing(); - } - else if( javax.swing.SwingUtilities.isRightMouseButton(evt)) - { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null); - pop.show(this, evt.getX(), evt.getY()); + av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); - // edit the properties of existing group } - if(stretchGroup!=null && stretchGroup.getEndRes()==res) - // Edit end res position of selected group - changeEndRes = true; + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMousePressedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int seq = findSeq(evt); + oldSeq = seq; - else if(stretchGroup!=null && stretchGroup.getStartRes()==res) - // Edit end res position of selected group - changeStartRes = true; + startWrapBlock=wrappedBlock; - stretchGroup.getWidth(); + if(av.wrapAlignment && seq>av.alignment.getHeight()) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Cannot edit annotations in wrapped view.", + "Wrapped view - no edit", + JOptionPane.WARNING_MESSAGE); + return; + } - repaint(); + if(seq<0 || res<0) + return; - } + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); - boolean changeEndSeq = false; - boolean changeStartSeq = false; - boolean changeEndRes = false; - boolean changeStartRes = false; - SequenceGroup stretchGroup = null; + if ((sequence == null) || (res > sequence.getLength())) + { + return; + } - public void doMouseReleasedDefineMode(MouseEvent evt) - { - mouseDragging = false; + stretchGroup = av.getSelectionGroup(); - if(stretchGroup==null) - return; + if (stretchGroup == null) + { + stretchGroup = av.alignment.findGroup(sequence); - if(stretchGroup.cs instanceof ClustalxColourScheme) - { - stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth()); - repaint(); - } + if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && + (res < stretchGroup.getEndRes())) + { + av.setSelectionGroup(stretchGroup); + } + else + { + stretchGroup = null; + } + } + else if (!stretchGroup.sequences.contains(sequence) || + (stretchGroup.getStartRes() > res) || + (stretchGroup.getEndRes() < res)) + { + stretchGroup = null; - else if(stretchGroup.cs instanceof ConservationColourScheme) - { - ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs; - stretchGroup.cs = ccs; - SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ; + SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); - repaint(); - } - else - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName()); + if (allGroups != null) + { + for (int i = 0; i < allGroups.length; i++) + { + if ((allGroups[i].getStartRes() <= res) && + (allGroups[i].getEndRes() >= res)) + { + stretchGroup = allGroups[i]; + av.setSelectionGroup(stretchGroup); + + break; + } + } + } + } + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } - changeEndRes = false; - changeStartRes = false; - stretchGroup = null; - ap.idPanel.repaint(); - } + if (stretchGroup == null) + { + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), "Background"); + } - boolean remove = false; - public void doMouseDraggedDefineMode(MouseEvent evt) - { - int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - int y = evt.getY()/av.getCharHeight() + av.getStartSeq(); + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); + } + } + else if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + { + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null); + pop.show(this, evt.getX(), evt.getY()); - if(stretchGroup==null) - return; + // edit the properties of existing group + } - if(res>av.alignment.getWidth()) - res = av.alignment.getWidth()-1; + if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); - if(stretchGroup.getEndRes()==res) - // Edit end res position of selected group - changeEndRes = true; + seqCanvas.repaint(); + } - else if(stretchGroup.getStartRes()==res) - // Edit start res position of selected group - changeStartRes = true; + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseReleasedDefineMode(MouseEvent evt) + { + if (stretchGroup == null) + { + return; + } - if(resav.getEndRes()) - res = av.getEndRes(); + if(stretchGroup.cs!=null) + { + if (stretchGroup.cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup. + sequences, + stretchGroup.getWidth()); + } - if(changeEndRes) - { - if(res>stretchGroup.getStartRes()-1) - stretchGroup.setEndRes( res ); - } - else if(changeStartRes) - { - if(res oldSeq) - dragDirection = 1; - else if (y < oldSeq) - dragDirection = -1; - - while (y != oldSeq && oldSeq>0 && y av.alignment.getHeight()) + { + y = av.alignment.getHeight() -1; + } + if(res> av.alignment.getWidth()) + { + res = av.alignment.getWidth()-1; + } - public void doMouseExitedDefineMode(MouseEvent e) - { - if (av.getWrapAlignment()) - return; + if (stretchGroup.getEndRes() == res) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if (stretchGroup.getStartRes() == res) + { + // Edit start res position of selected group + changeStartRes = true; + } - if(mouseDragging) - scrollThread = new ScrollThread(); + if (res < av.getStartRes()) + { + res = av.getStartRes(); + } - } - // this class allows scrolling off the bottom of the visible alignment - class ScrollThread extends Thread - { - MouseEvent evt; - boolean running = false; - public ScrollThread() - { - start(); - } + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) + { + stretchGroup.setEndRes(res); + } + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) + { + stretchGroup.setStartRes(res); + } + } - public void setEvent(MouseEvent e) - { - evt = e; - } + int dragDirection = 0; - public void stopScrolling() - { - running = false; - } + if (y > oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } - public void run() - { - running = true; - while (running) - { - if(evt!=null) + + while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) { + // This routine ensures we don't skip any sequences, as the + // selection is quite slow. + Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0) - running = ap.scrollUp(true); + oldSeq += dragDirection; - if (mouseDragging && evt.getY() >= getHeight() && - av.alignment.getHeight() > av.getEndSeq()) - running = ap.scrollUp(false); + if(oldSeq<0) + break; - if (mouseDragging && evt.getX() < 0) - running = ap.scrollRight(true); + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - else if (mouseDragging && evt.getX() >= getWidth()) - running = ap.scrollRight(false); + if (stretchGroup.sequences.contains(nextSeq)) + { + stretchGroup.deleteSequence(seq, false); + } + else + { + if (seq != null) + { + stretchGroup.addSequence(seq, false); + } + + stretchGroup.addSequence(nextSeq, false); + } } - try + if(oldSeq < 0) + oldSeq = -1; + + mouseDragging = true; + + if (scrollThread != null) { - Thread.sleep(75); + scrollThread.setEvent(evt); } - catch (Exception ex) - {} + + seqCanvas.repaint(); + } + + void scrollCanvas(MouseEvent evt) + { + if(evt==null) + { + if(scrollThread!=null) + { + scrollThread.running = false; + scrollThread = null; + } + mouseDragging = false; + } + else + { + if (scrollThread == null) + scrollThread = new ScrollThread(); + + mouseDragging = true; + scrollThread.setEvent(evt); } + } -} + // this class allows scrolling off the bottom of the visible alignment + class ScrollThread extends Thread + { + MouseEvent evt; + boolean running = false; -} + public ScrollThread() + { + start(); + } + public void setEvent(MouseEvent e) + { + evt = e; + } + public void stopScrolling() + { + running = false; + } + public void run() + { + running = true; + while (running) + { + if (evt != null) + { + if (mouseDragging && (evt.getY() < 0) && + (av.getStartSeq() > 0)) + { + running = ap.scrollUp(true); + } + + if (mouseDragging && (evt.getY() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) + { + running = ap.scrollUp(false); + } + + if (mouseDragging && (evt.getX() < 0)) + { + running = ap.scrollRight(false); + } + else if (mouseDragging && (evt.getX() >= getWidth())) + { + running = ap.scrollRight(true); + } + } + + try + { + Thread.sleep(20); + } + catch (Exception ex) + { + } + } + } + } +}