X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=89e2086a1ebbd81a81e2f2286dc7071a3fc7455c;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=163b96705b536f2a87324468237460c802581ed6;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 163b967..89e2086 100755 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,153 +1,500 @@ /* -* 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2006 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.appletgui; import java.awt.*; import java.awt.event.*; + import jalview.datamodel.*; -import java.util.*; import jalview.schemes.*; +import jalview.commands.*; +import java.util.Vector; -public class SeqPanel extends Panel +public class SeqPanel + extends Panel implements MouseMotionListener, MouseListener { - public SeqCanvas seqCanvas; - public AlignmentPanel ap; + public SeqCanvas seqCanvas; + public AlignmentPanel ap; protected int lastres; protected int startseq; - int startEdit=-1; - int endEdit=-1; protected AlignViewport av; // if character is inserted or deleted, we will need to recalculate the conservation - int seqEditOccurred = -1; + boolean seqEditOccurred = false; ScrollThread scrollThread = null; boolean mouseDragging = false; - boolean editingSeqs = false; boolean groupEditing = false; + int oldSeq = -1; + boolean changeEndSeq = false; + boolean changeStartSeq = false; + boolean changeEndRes = false; + boolean changeStartRes = false; + SequenceGroup stretchGroup = null; + + StringBuffer keyboardNo1; + StringBuffer keyboardNo2; + boolean mouseWheelPressed = false; + Point lastMousePress; - public SeqPanel(AlignViewport avp, AlignmentPanel p) { - this.av = avp; + EditCommand editCommand; + + public SeqPanel(AlignViewport avp, AlignmentPanel p) + { + this.av = avp; - seqCanvas = new SeqCanvas(avp); + seqCanvas = new SeqCanvas(avp); setLayout(new BorderLayout()); add(seqCanvas); ap = p; - seqCanvas.addMouseMotionListener( new MouseMotionAdapter() + seqCanvas.addMouseMotionListener(this); + seqCanvas.addMouseListener(this); + + seqCanvas.repaint(); + } + + void endEditing() + { + if (editCommand!=null && editCommand.getSize() > 0) { - public void mouseMoved(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - doMouseMoved(evt); } + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); + } - public void mouseDragged(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - if( editingSeqs ) - doMouseDragged(evt); - else - doMouseDraggedDefineMode(evt); + startseq = -1; + lastres = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = null; + } + + void setCursorRow() + { + seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorRowAndColumn() + { + if(keyboardNo2==null) + { + keyboardNo2 = new StringBuffer(); + } + else + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; + seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; + scrollToVisible(); + } + } + + void setCursorPosition() + { + 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; + if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) + { + int original = seqCanvas.cursorX - dx; + int maxWidth = av.alignment.getWidth(); + + while(!av.colSel.isVisible(seqCanvas.cursorX) + && seqCanvas.cursorX0) + { + seqCanvas.cursorX += dx; + } + + if(seqCanvas.cursorX>=maxWidth + || !av.colSel.isVisible(seqCanvas.cursorX) ) + { + seqCanvas.cursorX = original; + } } - }); + scrollToVisible(); + } - seqCanvas.addMouseListener( new MouseAdapter() - { - public void mouseReleased(MouseEvent evt) - { - if(av.getWrapAlignment()) + 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(); + if (av.wrapAlignment) + { + ap.scrollToWrappedVisible(seqCanvas.cursorX); + } + else + { + while (seqCanvas.cursorY < av.startSeq) + { + ap.scrollUp(true); + } + while (seqCanvas.cursorY + 1 > av.endSeq) + { + ap.scrollUp(false); + } + while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes)) + { + + if (!ap.scrollRight(false)) + break; + } + while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes)) + { + if (!ap.scrollRight(true)) + break; + } + } + setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + seqCanvas.cursorX, seqCanvas.cursorY); + + seqCanvas.repaint(); + } + + void setSelectionAreaAtCursor(boolean topLeft) + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + + 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; + } + + max ++; + + if(topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if(sg.getEndRes()seqCanvas.cursorX) + sg.setStartRes(seqCanvas.cursorX); + + max = seqCanvas.cursorY+1; + } + + if(min>max) + { + // Only the user can do this + av.setSelectionGroup(null); + } + else + { + // Now add any sequences between min and max + sg.getSequences(null).removeAllElements(); + 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); + } + + + ap.repaint(); + } + + void insertGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); + endEditing(); + } + + void deleteGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); + editSequence(false, seqCanvas.cursorX); + endEditing(); + } + + void numberPressed(char value) + { + if(keyboardNo1==null) + keyboardNo1 = new StringBuffer(); + + if(keyboardNo2!=null) + keyboardNo2.append(value); + else + keyboardNo1.append(value); + } + + int getKeyboardNo(StringBuffer kb) + { + if(kb==null) + return 1; + else + return Integer.parseInt(kb.toString()); + } + + 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()); + + } + public void mousePressed(MouseEvent evt) + { + lastMousePress = evt.getPoint(); + + //For now, ignore the mouseWheel font resizing on Macs + //As the Button2_mask always seems to be true + if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) == + InputEvent.BUTTON2_MASK && !av.MAC) + { + mouseWheelPressed = true; return; - if(editingSeqs) - doMouseReleased(evt); - else - doMouseReleasedDefineMode(evt); + } - } - public void mousePressed(MouseEvent evt) - { - if(av.getWrapAlignment()) + if (evt.isShiftDown() + || evt.isControlDown() + || evt.isAltDown()) + { + if (evt.isControlDown() || evt.isAltDown()) + { + groupEditing = true; + } + editingSeqs = true; + } + else + { + doMousePressedDefineMode(evt); return; - if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) - { - if(evt.isAltDown() || evt.isControlDown()) - groupEditing = true; + } - editingSeqs = true; - doMousePressed(evt); - } - else - doMousePressedDefineMode(evt); - } - public void mouseExited(MouseEvent evt) - { - if (av.getWrapAlignment() || editingSeqs) - return; - doMouseExitedDefineMode(evt); - } - public void mouseEntered(MouseEvent evt) - { - if (av.getWrapAlignment() || editingSeqs) - return; - doMouseEnteredDefineMode(evt); - } + int seq = findSeq(evt); + int res = findRes(evt); - }); - seqCanvas.repaint(); + if(seq<0 || res<0) + return; + + + if ((seq < av.getAlignment().getHeight()) && + (res < av.getAlignment().getSequenceAt(seq).getLength())) + { + startseq = seq; + lastres = res; + } + else + { + startseq = -1; + lastres = -1; + } + + return; + } + + public void mouseClicked(MouseEvent evt){} + + + public void mouseReleased(MouseEvent evt) + { + mouseDragging = false; + mouseWheelPressed = false; + + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } + + endEditing(); + ap.repaint(); } + int startWrapBlock=-1; + int wrappedBlock=-1; + int findRes(MouseEvent evt) + { + int res = 0; + int x = evt.getX(); - public void doMouseReleased(MouseEvent evt) { + if (av.wrapAlignment) + { - if(seqEditOccurred>-1) - editOccurred(seqEditOccurred); + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - startseq = -1; - lastres = -1; - seqEditOccurred = -1; - editingSeqs = false; - groupEditing = false; - ap.repaint(); + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); + + int y = evt.getY(); + y -= hgap; + x -= seqCanvas.LABEL_WEST; + + + int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width); + if(cwidth<1) + return 0; + + wrappedBlock = y / cHeight; + wrappedBlock += av.getStartRes() / cwidth; + + res = wrappedBlock * cwidth + x / av.getCharWidth(); + + } + else + { + res = (x / av.getCharWidth()) + av.getStartRes(); } - public void doMousePressed(MouseEvent evt) { - ap.alignFrame.addHistoryItem( new HistoryItem( - "Edit Sequence",av.alignment, HistoryItem.EDIT)); - int seq; - int res; + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + + return res; + + } + + int findSeq(MouseEvent evt) + { - int x = evt.getX(); - int y = evt.getY(); + int seq = 0; + int y = evt.getY(); - res = x/av.getCharWidth() + av.getStartRes(); - seq = y/av.getCharHeight() + av.getStartSeq(); + 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; + + seq = Math.min( (y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() -1); + if(seq<0) + seq = 0; + } + else + { + seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), + av.alignment.getHeight() -1); + if(seq<0) + seq = 0; + } + + return seq; + } + + + public void doMousePressed(MouseEvent evt) + { + + int seq = findSeq(evt); + int res = findRes(evt); if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength()) @@ -168,474 +515,921 @@ public class SeqPanel extends Panel return; } - public void doMouseMoved(MouseEvent evt) + public void mouseMoved(MouseEvent evt) { - int res=0, seq=0; - int x = evt.getX(); - int y = evt.getY(); - if(av.wrapAlignment) - { - y -= 2*av.charHeight; - int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight; + int res = findRes(evt); + int seq = findSeq(evt); + if (seq >= av.getAlignment().getHeight() || seq<0 || res<0) + { + return; + } - res = (int)((y/chunkHeight)*(getSize().width/av.charWidth)) + x/av.getCharWidth() + av.getStartRes(); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + if (res > sequence.getLength()) + { + return; + } - y %= chunkHeight; - seq = y / av.getCharHeight() + av.getStartSeq(); + 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 { - res = x / av.getCharWidth() + av.getStartRes(); - seq = y / av.getCharHeight() + av.getStartSeq(); + obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + if(obj!=null) + text.append(" Residue: "); } + if (obj != null) + { + if (obj != "") + { + text.append(obj + " (" + sequence.findPosition(res) + ")"); + } + } - 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(); - - StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName()); - if(aa!="") - text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")"); + if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) + { + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + } ap.alignFrame.statusBar.setText(text.toString()); + // use aa to see if the mouse pointer is on a - if( av.showSequenceFeatures) + if (av.showSequenceFeatures + && sequence.getSequenceFeatures()!=null + && av.featuresDisplayed!=null) { - Vector features = sequence.getSequenceFeatures(); - Enumeration e = features.elements(); - StringBuffer sbuffer = new StringBuffer(); - + StringBuffer featureText = new StringBuffer(); + Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res)); - while (e.hasMoreElements()) + int index = 0; + while (index < allFeatures.size()) { - SequenceFeature sf = (SequenceFeature) e.nextElement(); - if (sf.getStart() <= sequence.findPosition(res) && - sf.getEnd() >= sequence.findPosition(res)) + SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index); + + featureText.append(sf.getType()+" "+sf.begin+":"+sf.end); + + if (sf.getDescription() != null) + featureText.append(" " + sf.getDescription()); + + if (sf.getValue("status") != null ) { - if(sbuffer.length()>0) - sbuffer.append("; "); - sbuffer.append(sf.getType() + " " + sf.getDescription()); - if(sf.getStatus().length()>0) - sbuffer.append(" ("+sf.getStatus()+")"); + String status = sf.getValue("status").toString(); + if(status.length()>0) + featureText.append(" (" + sf.getValue("status") + ")"); } + featureText.append("\n"); + index++; } - } + if (tooltip == null) + tooltip = new Tooltip(featureText.toString(), seqCanvas); + else + tooltip.setTip(featureText.toString()); + + tooltip.repaint(); + + } + else if (tooltip != null) + { + tooltip.setTip(""); + } } - public void doMouseDragged(MouseEvent evt) { + Vector getAllFeaturesAtRes(SequenceI seq, int res) + { + Vector allFeatures = new Vector(); + int index = 0; + if(seq.getSequenceFeatures()!=null) + { + while (index < seq.getSequenceFeatures().length) + { + SequenceFeature sf = seq.getSequenceFeatures()[index]; + if (sf.getBegin() <= res && + sf.getEnd() >= res) + { + if (av.featuresDisplayed.containsKey(sf.getType())) + { + allFeatures.addElement(sf); + } + } + index++; + } + } + return allFeatures; + } - // If we're dragging we're editing - int res = evt.getX() / av.getCharWidth() + av.getStartRes(); - if (res < 0) - res = 0; + Tooltip tooltip; - if (lastres == -1 || lastres == res) - return; + public void mouseDragged(MouseEvent evt) + { + if (mouseWheelPressed) + { + int oldWidth = av.charWidth; - boolean dragRight = true; - if (res < av.getAlignment().getWidth() && res < lastres) - dragRight = false; + //Which is bigger, left-right or up-down? + if (Math.abs(evt.getY() - lastMousePress.y) + > Math.abs(evt.getX() - lastMousePress.x)) + { + int fontSize = av.font.getSize(); + if (evt.getY() < lastMousePress.y && av.charHeight > 1) + { + fontSize--; + } + else if (evt.getY() > lastMousePress.y) + { + fontSize++; + } - if (res != lastres) - { - // Group editing - if (groupEditing) - { - SequenceGroup sg = av.getSelectionGroup(); - if(sg==null) - { - lastres=-1; - return; - } - // drag to right - if(dragRight) - sg.setEndRes(sg.getEndRes() + (res-lastres)); - - // drag to left - else - { - /// Are we able to delete? - // ie are all columns blank? - boolean deleteAllowed = false; - for (int s = 0; s < sg.getSize(); s++) - { - SequenceI seq = sg.getSequenceAt(s); - for (int j=res; jj) - deleteChar(res, k); - } - } - } - } - else /////Editing a single sequence/////////// - { - if (res < av.getAlignment().getWidth() && res > lastres) - { - // dragging to the right - for (int j = lastres; j < res; j++) - insertChar(j, startseq); - } - else if (res < av.getAlignment().getWidth() && res < lastres) - { - // dragging to the left - for (int j = lastres; j > res; j--) - { - if( jalview.util.Comparison.isGap( - av.alignment.getSequenceAt(startseq).getSequence().charAt(res))) - - deleteChar(res, startseq); - else - { - - break; - } - } - } + if(fontSize<1) + fontSize = 1; - } - } + av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); + av.charWidth = oldWidth; + } + else + { + if (evt.getX() < lastMousePress.x && av.charWidth > 1) + { + av.charWidth--; + } + else if (evt.getX() > lastMousePress.x) + { + av.charWidth++; + } - endEdit = res; - lastres = res; - seqCanvas.repaint(); + if(av.charWidth<1) + { + av.charWidth = 1; + } + } + + ap.fontChanged(); + + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.charWidth; + + lastMousePress = evt.getPoint(); + + ap.repaint(); + ap.annotationPanel.image = null; + return; + } + + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } + + int res = findRes(evt); + + if (res < 0) + { + res = 0; } - public void drawChars(int seqstart, int seqend, int start) { - seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0); - seqCanvas.repaint(); + if ((lastres == -1) || (lastres == res)) + { + return; } - public void insertChar(int j, int seq) + if ( (res < av.getAlignment().getWidth()) && (res < lastres)) { - av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred=seq; + // dragLeft, delete gap + editSequence(false, res); } + else + editSequence(true, res); - public void deleteChar(int j, int seq) + mouseDragging = true; + if(scrollThread!=null) + scrollThread.setEvent(evt); + + } + + synchronized void editSequence(boolean insertGap, int startres) { + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); - av.alignment.getSequenceAt(seq).deleteCharAt(j); - seqEditOccurred=seq; - av.alignment.getWidth(); - repaint(); + SequenceI seq = av.alignment.getSequenceAt(startseq); + + if (!groupEditing && av.hasHiddenRows) + { + if (av.hiddenRepSequences!=null + && av.hiddenRepSequences.containsKey(seq)) + { + sg = (SequenceGroup)av.hiddenRepSequences.get(seq); + groupEditing = true; + } + } + + StringBuffer message = new StringBuffer(); + if (groupEditing) + { + message.append("Edit group:"); + if (editCommand == null) + editCommand = new EditCommand("Edit Group"); + } + else + { + message.append("Edit sequence: " + seq.getName()); + String label = seq.getName(); + if(label.length()>10) + label = label.substring(0,10); + if(editCommand==null) + editCommand = new EditCommand("Edit "+label); + } + + 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.getSequences(av.hiddenRepSequences).contains(seq))) + { + fixedColumns = true; + + //sg might be null as the user may only see 1 sequence, + //but the sequence represents a group + if (sg == null) + { + sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + } + + fixedLeft = sg.getStartRes(); + fixedRight = sg.getEndRes(); + + if ( (startres < fixedLeft && lastres >= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <=fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) + { + endEditing(); + return; + } + + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } + } + + + if(av.hasHiddenColumns ) + { + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + + if ( (insertGap && startres > y1 && lastres < y1) + || (!insertGap && startres < y2 && lastres > y2)) + { + endEditing(); + return; + } + + //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + //Selection spans a hidden region + if(fixedLefty2 || fixedRight==-1)) + { + if(startres>=y2) + { + fixedLeft = y2; + } + else + { + fixedRight = y2 - 1; + } + } + } + + + if (groupEditing) + { + Vector vseqs = sg.getSequences(av.hiddenRepSequences); + int g, groupSize = vseqs.size(); + SequenceI[] groupSeqs = new SequenceI[groupSize]; + for (g = 0; g < groupSeqs.length; g++) + groupSeqs[g] = (SequenceI) vseqs.elementAt(g); + + // 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() == fixedRight + && sg.getEndRes() == av.alignment.getWidth()-1 + ) + { + 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 (g = 0; g < groupSize; g++) + { + for (int j = 0; j < startres - lastres; j++) + { + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(fixedRight - j))) + { + blank = false; + break; + } + } + } + if (blank) + break; + } + + if (!blank) + { + if(sg.getSize() == av.alignment.getHeight() ) + { + if((av.hasHiddenColumns + && startresalWidth) + alWidth = hwidth; + } + //We can still insert gaps if the selectionGroup + //contains all the sequences + sg.setEndRes(sg.getEndRes()+startres-lastres); + fixedRight = alWidth+startres-lastres; + } + else + { + endEditing(); + return; + } + } + } + + + // drag to left + else if(!insertGap) + { + /// Are we able to delete? + // ie are all columns blank? + + for (g = 0; g < groupSize; g++) + { + for (int j = startres; j < lastres; j++) + { + if (groupSeqs[g].getLength() <= j) + { + continue; + } + + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(j))) + { + // Not a gap, block edit not valid + endEditing(); + return; + } + } + } + } + + if (insertGap) + { + // dragging to the right + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, groupSeqs, fixedRight); + } + } + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + groupSeqs, + startres, startres-lastres, + av.getGapCharacter(), + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j > startres; j--) + { + deleteChar(startres, groupSeqs, fixedRight); + } + } + else + editCommand.appendEdit(EditCommand.DELETE_GAP, + groupSeqs, + startres, lastres - startres, + av.getGapCharacter(), + true); + + } + } + else /////Editing a single sequence/////////// + { + if (insertGap) + { + // dragging to the right + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, new SequenceI[]{seq}, fixedRight); + } + } + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + new SequenceI[] + {seq}, + lastres, startres-lastres, + av.getGapCharacter(), + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j > startres; j--) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + { + endEditing(); + break; + } + deleteChar(startres, new SequenceI[]{seq}, fixedRight); + } + } + else + { + //could be a keyboard edit trying to delete none gaps + int max=0; + for(int m = startres; m0) + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + new SequenceI[] + {seq}, + startres, max, + av.getGapCharacter(), + true); + } + } + } + } + + lastres = startres; + seqCanvas.repaint(); } - void editOccurred(int i) + + void insertChar(int j, SequenceI [] seq, int fixedColumn) { - if(endEdit==startEdit) + int blankColumn = fixedColumn; + for(int s=0; s j, theres a boundary after the gap insertion - av.updateConservation(); - av.updateConsensus(); + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) + { + if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } + } - // Y O Y CLUSTALX - ColourSchemeI cs = av.getGlobalColourScheme(); - if(cs instanceof ConservationColourScheme) - { - ConservationColourScheme ccs = (ConservationColourScheme) cs; - if(ccs.cs instanceof ClustalxColourScheme) - { - jalview.analysis.Conservation c = new jalview.analysis.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 (blankColumn <= j) + { + blankColumn = fixedColumn; + endEditing(); + return; + } } - if(cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(), - av.alignment.getWidth()); - av.setGlobalColourScheme(cs); - } + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + blankColumn, 1, av.getGapCharacter(), true); + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + j, 1, av.getGapCharacter(), + true); } + void deleteChar(int j, SequenceI [] seq, int fixedColumn) + { + + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + j, 1, av.getGapCharacter(), true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + fixedColumn, 1, av.getGapCharacter(), true); + } + + ////////////////////////////////////////// /////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(); + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } + + int res = findRes(evt); + int seq = findSeq(evt); oldSeq = seq; + startWrapBlock=wrappedBlock; + + if(seq==-1) + return; SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); - if(sequence==null || res>sequence.getLength()) + 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) + { + stretchGroup = av.alignment.findGroup(sequence); + if (stretchGroup != null && res > stretchGroup.getStartRes() && + res < stretchGroup.getEndRes()) + { + av.setSelectionGroup(stretchGroup); + } + else + { + stretchGroup = null; + } + } - if(stretchGroup==null) + else if (!stretchGroup.getSequences(null).contains(sequence) + || stretchGroup.getStartRes() > res + || stretchGroup.getEndRes() < res) { - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence( sequence ); - av.setSelectionGroup( sg ); - stretchGroup = sg; + stretchGroup = null; - if(av.getConservationSelected()) - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background"); - if(av.getAbovePIDThreshold()) - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background"); + SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + if (allGroups != null) + { + for (int i = 0; i < allGroups.length; i++) + { + if (allGroups[i].getStartRes() <= res && + allGroups[i].getEndRes() >= res) + { + stretchGroup = allGroups[i]; + break; + } + } + } + av.setSelectionGroup(stretchGroup); } + // DETECT RIGHT MOUSE BUTTON IN AWT - else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK ) + if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) == + InputEvent.BUTTON3_MASK) { - APopupMenu popup = new APopupMenu(ap, null); + Vector allFeatures = getAllFeaturesAtRes(sequence, + sequence.findPosition(res)); + + Vector links = null; + if(allFeatures!=null) + { + for (int i = 0; i < allFeatures.size(); i++) + { + SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); + if (sf.links != null) + { + links = new Vector(); + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); + } + } + } + } + APopupMenu popup = new APopupMenu(ap, null, links); this.add(popup); popup.show(this, evt.getX(), evt.getY()); + ap.repaint(); + return; } + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } - if(stretchGroup!=null && stretchGroup.getEndRes()==res) - // Edit end res position of selected group - changeEndRes = true; + //Only if left mouse button do we want to change group sizes - else if(stretchGroup!=null && stretchGroup.getStartRes()==res) - // Edit end res position of selected group - changeStartRes = true; + 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"); + } + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); + } + } } - boolean changeEndSeq = false; - boolean changeStartSeq = false; - boolean changeEndRes = false; - boolean changeStartRes = false; - SequenceGroup stretchGroup = null; - public void doMouseReleasedDefineMode(MouseEvent evt) { - mouseDragging = false; - - if(stretchGroup==null) - return; - - if(stretchGroup.cs instanceof ClustalxColourScheme) + if (stretchGroup == null) { - stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth()); - seqCanvas.repaint(); + return; } - else if(stretchGroup.cs instanceof ConservationColourScheme) - { - ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs; - stretchGroup.cs = ccs; - SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ; - - seqCanvas.repaint(); - } - else + if(stretchGroup.cs!=null) { - if(stretchGroup.cs !=null) + if (stretchGroup.cs instanceof ClustalxColourScheme) { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName()); + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(av.hiddenRepSequences), + stretchGroup.getWidth()); } - } + if (stretchGroup.cs instanceof Blosum62ColourScheme + || stretchGroup.cs instanceof PIDColourScheme + || stretchGroup.cs.conservationApplied() + || stretchGroup.cs.getThreshold() > 0) + stretchGroup.recalcConservation(); + if (stretchGroup.cs.conservationApplied()) + { + SliderPanel.setConservationSlider(ap, stretchGroup.cs, + stretchGroup.getName()); + stretchGroup.recalcConservation(); + } + else + { + SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, + stretchGroup.getName()); + } + } changeEndRes = false; changeStartRes = false; stretchGroup = null; + PaintRefresher.Refresh(ap, av.getSequenceSetId()); ap.repaint(); } - - boolean remove = false; public void doMouseDraggedDefineMode(MouseEvent evt) { - int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - int y = evt.getY()/av.getCharHeight() + av.getStartSeq(); + int res = findRes(evt); + int y = findSeq(evt); - if(stretchGroup==null) + if(wrappedBlock!=startWrapBlock) return; - if(res>av.alignment.getWidth()) - res = av.alignment.getWidth()-1; + if (stretchGroup == null) + { + return; + } + mouseDragging = true; - 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(y > av.alignment.getHeight()) + { + y = av.alignment.getHeight() -1; + } + if(res>=av.alignment.getWidth()) + res = av.alignment.getWidth()-1; - if(resav.getEndRes()) - res = av.getEndRes(); + 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(changeEndRes) - { - if(res>stretchGroup.getStartRes()-1) - stretchGroup.setEndRes( res ); - } - else if(changeStartRes) - { - if(res oldSeq) - dragDirection = 1; - else if (y < oldSeq) - dragDirection = -1; + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) + { + stretchGroup.setEndRes(res); + } + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) + { + stretchGroup.setStartRes(res); + } + } - while (y != oldSeq && oldSeq>0 && y oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } - if (stretchGroup.sequences.contains(nextSeq)) + + while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) { - stretchGroup.deleteSequence(seq); - stretchGroup.deleteSequence(nextSeq); + // This routine ensures we don't skip any sequences, as the + // selection is quite slow. + Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); + + oldSeq += dragDirection; + + if(oldSeq<0) + break; + + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); + + if (stretchGroup.getSequences(null).contains(nextSeq)) + { + stretchGroup.deleteSequence(seq, false); + } + else + { + if (seq != null) + { + stretchGroup.addSequence(seq, false); + } + + stretchGroup.addSequence(nextSeq, false); + } } - else + + if(oldSeq < 0) + oldSeq = -1; + + + if(res>av.endRes || resav.endSeq) + { + mouseExited(evt); + } + + if (scrollThread != null) { - if(seq!=null) - stretchGroup.addSequence(seq); - stretchGroup.addSequence(nextSeq); + scrollThread.setEvent(evt); } + + seqCanvas.repaint(); } - oldSeq = y; - mouseDragging = true; - if(scrollThread!=null) - scrollThread.setEvent(evt); - seqCanvas.repaint(); - } + public void mouseEntered(MouseEvent e) + { + if (oldSeq < 0) + oldSeq = 0; - public void doMouseEnteredDefineMode(MouseEvent e) - { - if (scrollThread != null) - scrollThread.running = false; - } + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } + } - public void doMouseExitedDefineMode(MouseEvent e) + public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) + { return; + } - if(mouseDragging) + if (mouseDragging && scrollThread==null) + { scrollThread = new ScrollThread(); - + } } + + 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 + class ScrollThread + extends Thread { MouseEvent evt; boolean running = false; @@ -659,21 +1453,30 @@ public class SeqPanel extends Panel running = true; while (running) { - if(evt!=null) + + if (evt != null) { if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0) + { running = ap.scrollUp(true); + } if (mouseDragging && evt.getY() >= getSize().height && av.alignment.getHeight() > av.getEndSeq()) + { running = ap.scrollUp(false); + } if (mouseDragging && evt.getX() < 0) - running = ap.scrollRight(true); + { + running = ap.scrollRight(false); + } else if (mouseDragging && evt.getX() >= getSize().width) - running = ap.scrollRight(false); + { + running = ap.scrollRight(true); + } } try @@ -684,12 +1487,6 @@ public class SeqPanel extends Panel {} } } -} - - + } } - - - -