X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=b0de2ae71f867a535338a069eab6af61bd388f54;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=d7f11bb23ab187b989850f672c450877e422f167;hpb=b90206d60dbcb530a3eeeb00b4802ba0a6d8bad2;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java old mode 100755 new mode 100644 index d7f11bb..b0de2ae --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,882 +1,1815 @@ -/* - * 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.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.schemes.*; - -public class SeqPanel - extends Panel -{ - - 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; - - ScrollThread scrollThread = null; - boolean mouseDragging = false; - - boolean editingSeqs = false; - boolean groupEditing = false; - - public SeqPanel(AlignViewport avp, AlignmentPanel p) - { - this.av = avp; - - seqCanvas = new SeqCanvas(avp); - setLayout(new BorderLayout()); - add(seqCanvas); - - ap = p; - - seqCanvas.addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { - doMouseMoved(evt); - } - - public void mouseDragged(MouseEvent evt) - { - if (editingSeqs) - { - doMouseDragged(evt); - } - else - { - doMouseDraggedDefineMode(evt); - } - } - }); - - seqCanvas.addMouseListener(new MouseAdapter() - { - public void mouseReleased(MouseEvent evt) - { - if (editingSeqs) - { - doMouseReleased(evt); - } - else - { - doMouseReleasedDefineMode(evt); - } - - } - - public void mousePressed(MouseEvent evt) - { - 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 (editingSeqs) - { - return; - } - doMouseExitedDefineMode(evt); - - } - - public void mouseEntered(MouseEvent evt) - { - if (editingSeqs) - { - return; - } - doMouseEnteredDefineMode(evt); - } - - }); - seqCanvas.repaint(); - } - - public void doMouseReleased(MouseEvent evt) - { - - if (seqEditOccurred > -1) - { - editOccurred(seqEditOccurred); - } - - startseq = -1; - lastres = -1; - seqEditOccurred = -1; - editingSeqs = false; - groupEditing = false; - ap.repaint(); - } - - int startWrapBlock=-1; - int wrappedBlock=-1; - int findRes(MouseEvent evt) - { - int res = 0; - int x = evt.getX(); - - if (av.wrapAlignment) - { - int y = evt.getY(); - y -= (2 * av.charHeight); - x -= seqCanvas.LABEL_WEST; - - int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; - int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width); - wrappedBlock = y/chunkHeight; - wrappedBlock += av.getStartRes()/cwidth; - - res = wrappedBlock*cwidth + x / av.getCharWidth(); - } - else - { - res = (x / av.getCharWidth()) + av.getStartRes(); - } - - return res; - - } - - int findSeq(MouseEvent evt) - { - int seq = 0; - int y = evt.getY(); - - if (av.wrapAlignment) - { - y -= (2 * av.charHeight); - int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; - seq = ( (y % chunkHeight) / av.getCharHeight()); - } - else - { - seq = (y / av.getCharHeight()) + av.getStartSeq(); - } - - return seq; - } - - - public void doMousePressed(MouseEvent evt) - { - ap.alignFrame.addHistoryItem(new HistoryItem( - "Edit Sequence", av.alignment, HistoryItem.EDIT)); - - int seq = findSeq(evt); - int res = findRes(evt); - - if (seq < av.getAlignment().getHeight() && - res < av.getAlignment().getSequenceAt(seq).getLength()) - { - //char resstr = align.getSequenceAt(seq).getSequence().charAt(res); - // Find the residue's position in the sequence (res is the position - // in the alignment - - startseq = seq; - lastres = res; - } - else - { - startseq = -1; - lastres = -1; - } - - return; - } - - public void doMouseMoved(MouseEvent evt) - { - int res = findRes(evt); - int seq = findSeq(evt); - - if (seq >= av.getAlignment().getHeight() || seq<0 || res<0) - { - 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) + ")"); - } - - ap.alignFrame.statusBar.setText(text.toString()); - - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) - { - Vector features = sequence.getSequenceFeatures(); - Enumeration e = features.elements(); - StringBuffer sbuffer = new StringBuffer(); - - while (e.hasMoreElements()) - { - SequenceFeature sf = (SequenceFeature) e.nextElement(); - if (sf.getStart() <= sequence.findPosition(res) && - sf.getEnd() >= sequence.findPosition(res)) - { - if (sbuffer.length() > 0) - { - sbuffer.append("; "); - } - sbuffer.append(sf.getType() + " " + sf.getDescription()); - if (sf.getStatus().length() > 0) - { - sbuffer.append(" (" + sf.getStatus() + ")"); - } - } - - } - } - - } - - public void doMouseDragged(MouseEvent evt) - { - - // If we're dragging we're editing - int res = findRes(evt); - if (res < 0) - { - res = 0; - } - - if (lastres == -1 || lastres == res) - { - return; - } - - boolean dragRight = true; - if (res < av.getAlignment().getWidth() && res < lastres) - { - dragRight = false; - } - - 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; j < lastres; j++) - { - if (seq.getSequence().length() <= j) - { - continue; - } - - if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j))) - { - // Not a gap, block edit not valid - res = j + 1; - deleteAllowed = false; - continue; - } - deleteAllowed = true; - } - } - - if (!deleteAllowed) - { - lastres = -1; - return; - } - - sg.setEndRes(sg.getEndRes() - (lastres - res)); - } - - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI s = sg.getSequenceAt(i); - int k = av.alignment.findIndex(s); - - // drag to right - if (dragRight) - { - for (int j = lastres; j < res; j++) - { - insertChar(j, k); - } - } - - // drag to left - else - { - for (int j = res; j < lastres; j++) - { - if (s.getLength() > j) - { - 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; - } - } - } - - } - } - - endEdit = res; - lastres = res; - seqCanvas.repaint(); - } - - 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(); - } - - public void insertChar(int j, int seq) - { - av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = seq; - } - - public void deleteChar(int j, int seq) - { - - av.alignment.getSequenceAt(seq).deleteCharAt(j); - seqEditOccurred = seq; - av.alignment.getWidth(); - repaint(); - } - - void editOccurred(int i) - { - if (endEdit == startEdit) - { - ap.alignFrame.historyList.pop(); - ap.alignFrame.updateEditMenuBar(); - } - - av.updateConservation(); - av.updateConsensus(); - - - //Does the edit affect any groups? - ////////////////////////////// - Vector groupsToUpdate = new Vector(); - SequenceGroup sg = av.getSelectionGroup(); - - int s, g, gSize = av.alignment.getGroups().size(); - if (sg != null) - { - groupsToUpdate.addElement(av.getSelectionGroup()); - int sSize = sg.getSize(); - for (s = 0; s < sSize; s++) - { - SequenceI seq = sg.getSequenceAt(s); - - for (g = 0; g < gSize; g++) - { - SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups(). - elementAt( - g); - if (sg2.sequences.contains(seq)) - { - if (!groupsToUpdate.contains(sg2)) - groupsToUpdate.addElement(sg2); - continue; - } - } - } - } - else - { - SequenceI seq = av.alignment.getSequenceAt(startseq); - for (g = 0; g < gSize; g++) - { - SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt( - g); - if (sg2.sequences.contains(seq)) - { - if (!groupsToUpdate.contains(sg2)) - groupsToUpdate.addElement(sg2); - continue; - } - } - } - - gSize = groupsToUpdate.size(); - for (g = 0; g < gSize; g++) - { - ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation(); - } - ////End of updating groups - ////////////////////////////////////////// - - - // Y O Y CLUSTALX - ColourSchemeI cs = av.getGlobalColourScheme(); - - if (av.getSelectionGroup() != null) - { - av.getSelectionGroup().recalcConservation(); - } - - if(cs!=null) - { - if (cs.conservationApplied()) - { - 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); - - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme)cs). - resetClustalX(av.alignment.getSequences(), - av.alignment.getWidth()); - cs.setConservation(c); - av.setGlobalColourScheme(cs); - } - else - { - cs.setConservation(c); - av.setGlobalColourScheme(cs); - } - - } - - if (cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(), - av.alignment.getWidth()); - av.setGlobalColourScheme(cs); - } - } - } - -////////////////////////////////////////// -/////Everything below this is for defining the boundary of the rubberband -////////////////////////////////////////// - int oldSeq = -1; - public void doMousePressedDefineMode(MouseEvent evt) - { - int res = findRes(evt); - int seq = findSeq(evt); - oldSeq = seq; - startWrapBlock=wrappedBlock; - - 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() && - res < stretchGroup.getEndRes()) - { - av.setSelectionGroup(stretchGroup); - } - else - { - stretchGroup = null; - } - } - - else if (!stretchGroup.sequences.contains(sequence) - || stretchGroup.getStartRes() > res - || stretchGroup.getEndRes() < res) - { - stretchGroup = null; - - 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]; - av.setSelectionGroup(stretchGroup); - break; - } - } - } - } - - 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"); - } - - } - - // DETECT RIGHT MOUSE BUTTON IN AWT - else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) == - InputEvent.BUTTON3_MASK) - { - APopupMenu popup = new APopupMenu(ap, null, null); - this.add(popup); - popup.show(this, evt.getX(), evt.getY()); - } - - 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; - } - - } - - boolean changeEndSeq = false; - boolean changeStartSeq = false; - boolean changeEndRes = false; - boolean changeStartRes = false; - SequenceGroup stretchGroup = null; - - public void doMouseReleasedDefineMode(MouseEvent evt) - { - if(mouseDragging) - { - stretchGroup.recalcConservation(); - mouseDragging = false; - } - - if (stretchGroup == null) - { - return; - } - - if(stretchGroup.cs!=null) - { - if (stretchGroup.cs.conservationApplied()) - { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, - stretchGroup.getName()); - } - else - { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); - } - } - changeEndRes = false; - changeStartRes = false; - stretchGroup = null; - seqCanvas.repaint(); - ap.repaint(); - } - - boolean remove = false; - public void doMouseDraggedDefineMode(MouseEvent evt) - { - int res = findRes(evt); - int y = findSeq(evt); - - if(wrappedBlock!=startWrapBlock) - return; - - if(y>=av.alignment.getHeight()) - y = av.alignment.getHeight()-1; - - if (stretchGroup == null) - { - return; - } - - if (res > av.alignment.getWidth()) - { - res = av.alignment.getWidth() - 1; - } - - 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 (res < av.getStartRes()) - { - res = av.getStartRes(); - } - else if (res > av.getEndRes() && !av.getWrapAlignment()) - { - res = av.getEndRes(); - } - - if (changeEndRes) - { - if (res > stretchGroup.getStartRes() - 1) - { - stretchGroup.setEndRes(res); - } - } - else if (changeStartRes) - { - if (res < stretchGroup.getEndRes() + 1) - { - stretchGroup.setStartRes(res); - } - } - - int dragDirection = 0; - if (y > oldSeq) - { - dragDirection = 1; - } - else if (y < oldSeq) - { - dragDirection = -1; - } - - while (y != oldSeq && oldSeq > 0 && 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); - - oldSeq += dragDirection; - Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - - if (stretchGroup.sequences.contains(nextSeq)) - { - stretchGroup.deleteSequence(seq, false); - } - else - { - if (seq != null) - { - stretchGroup.addSequence(seq, false); - } - stretchGroup.addSequence(nextSeq, false); - } - } - oldSeq = y; - mouseDragging = true; - if (scrollThread != null) - { - scrollThread.setEvent(evt); - } - - seqCanvas.repaint(); - } - - public void doMouseEnteredDefineMode(MouseEvent e) - { - if (scrollThread != null) - { - scrollThread.running = false; - } - } - - public void doMouseExitedDefineMode(MouseEvent e) - { - if (mouseDragging) - { - scrollThread = new ScrollThread(); - } - } - - // 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() >= getSize().height && - av.alignment.getHeight() > av.getEndSeq()) - { - running = ap.scrollUp(false); - } - - if (mouseDragging && evt.getX() < 0) - { - running = ap.scrollRight(true); - } - - else if (mouseDragging && evt.getX() >= getSize().width) - { - running = ap.scrollRight(false); - } - } - - try - { - Thread.sleep(75); - } - catch (Exception ex) - {} - } - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . + */ +package jalview.appletgui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.schemes.*; +import jalview.structure.SelectionSource; +import jalview.structure.SequenceListener; +import jalview.structure.StructureSelectionManager; + +public class SeqPanel extends Panel implements MouseMotionListener, + MouseListener, SequenceListener +{ + + public SeqCanvas seqCanvas; + + 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; + + 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; + + EditCommand editCommand; + + StructureSelectionManager ssm; + + public SeqPanel(AlignViewport avp, AlignmentPanel p) + { + this.av = avp; + + seqCanvas = new SeqCanvas(avp); + setLayout(new BorderLayout()); + add(seqCanvas); + + ap = p; + + seqCanvas.addMouseMotionListener(this); + seqCanvas.addMouseListener(this); + ssm = StructureSelectionManager.getStructureSelectionManager(av.applet); + ssm.addStructureViewerListener(this); + + seqCanvas.repaint(); + } + + void endEditing() + { + if (editCommand != null && editCommand.getSize() > 0) + { + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, av.getAlignment() + .getSequences()); + } + + startseq = -1; + lastres = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = null; + } + + void setCursorRow() + { + seqCanvas.cursorY = getKeyboardNo1() - 1; + scrollToVisible(); + } + + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo1() - 1; + scrollToVisible(); + } + + void setCursorRowAndColumn() + { + if (keyboardNo2 == null) + { + keyboardNo2 = new StringBuffer(); + } + else + { + seqCanvas.cursorX = getKeyboardNo1() - 1; + seqCanvas.cursorY = getKeyboardNo2() - 1; + scrollToVisible(); + } + } + + void setCursorPosition() + { + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( + seqCanvas.cursorY); + + seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 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.cursorX < maxWidth && seqCanvas.cursorX > 0) + { + seqCanvas.cursorX += dx; + } + + if (seqCanvas.cursorX >= maxWidth + || !av.colSel.isVisible(seqCanvas.cursorX)) + { + seqCanvas.cursorX = original; + } + } + 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(); + 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 < sg.getSize(); i++) + { + int index = av.alignment.findIndex(sg.getSequenceAt(i)); + if (index > max) + { + max = index; + } + if (index < min) + { + min = index; + } + } + + max++; + + if (topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if (sg.getEndRes() < seqCanvas.cursorX) + { + sg.setEndRes(seqCanvas.cursorX); + } + + min = seqCanvas.cursorY; + } + else + { + sg.setEndRes(seqCanvas.cursorX); + if (sg.getStartRes() > 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.paintAlignment(false); + av.sendSelection(); + } + + void insertGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX + getKeyboardNo1()); + endEditing(); + } + + void deleteGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX + getKeyboardNo1(); + 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 getKeyboardNo1() + { + if (keyboardNo1 == null) + return 1; + else + { + int value = Integer.parseInt(keyboardNo1.toString()); + keyboardNo1 = null; + return value; + } + } + + int getKeyboardNo2() + { + if (keyboardNo2 == null) + return 1; + else + { + int value = Integer.parseInt(keyboardNo2.toString()); + keyboardNo2 = null; + return value; + } + } + + 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 (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown()) + { + if (evt.isControlDown() || evt.isAltDown()) + { + groupEditing = true; + } + editingSeqs = true; + } + else + { + doMousePressedDefineMode(evt); + return; + } + + int seq = findSeq(evt); + int res = findRes(evt); + + 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) + { + SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt)); + if (evt.getClickCount() > 1) + { + if (av.getSelectionGroup().getSize() == 1 + && av.getSelectionGroup().getEndRes() + - av.getSelectionGroup().getStartRes() < 2) + { + av.setSelectionGroup(null); + } + + SequenceFeature[] features = findFeaturesAtRes(sequence, + sequence.findPosition(findRes(evt))); + + if (features != null && features.length > 0) + { + SearchResults highlight = new SearchResults(); + highlight.addResult(sequence, features[0].getBegin(), + features[0].getEnd()); + seqCanvas.highlightSearchResults(highlight); + } + if (features != null && features.length > 0) + { + seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] + { sequence }, features, false, ap); + + seqCanvas.highlightSearchResults(null); + } + } + } + + public void mouseReleased(MouseEvent evt) + { + mouseDragging = false; + mouseWheelPressed = false; + ap.paintAlignment(true); + + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } + + endEditing(); + + } + + int startWrapBlock = -1; + + int wrappedBlock = -1; + + int findRes(MouseEvent evt) + { + int res = 0; + int x = evt.getX(); + + if (av.wrapAlignment) + { + + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + { + hgap += av.charHeight; + } + + 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(); + } + + if (av.hasHiddenColumns) + { + res = av.getColumnSelection().adjustForHiddenColumns(res); + } + + return res; + + } + + int findSeq(MouseEvent evt) + { + final int sqnum = findAlRow(evt); + return (sqnum < 0) ? 0 : sqnum; + } + + /** + * + * @param evt + * @return row in alignment that was selected (or -1 for column selection) + */ + private int findAlRow(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; + + seq = Math.min((y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() - 1); + if (seq < 0) + { + seq = -1; + } + } + else + { + seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), + av.alignment.getHeight() - 1); + if (seq < 0) + { + seq = -1; + } + } + + 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()) + { + // char resstr = align.getSequenceAt(seq).getSequence().charAt(res); + // Find the residue's position in the sequence (res is the position + // in the alignment + + startseq = seq; + lastres = res; + } + else + { + startseq = -1; + lastres = -1; + } + + return; + } + + String lastMessage; + + public void mouseOverSequence(SequenceI sequence, int index, int pos) + { + String tmp = sequence.hashCode() + index + ""; + if (lastMessage == null || !lastMessage.equals(tmp)) + ssm.mouseOverSequence(sequence, index, pos, av); + + lastMessage = tmp; + } + + public void highlightSequence(SearchResults results) + { + if (av.followHighlight) + { + if (ap.scrollToPosition(results, true)) + { + ap.alignFrame.repaint(); + } + } + seqCanvas.highlightSearchResults(results); + + } + + public void updateColours(SequenceI seq, int index) + { + System.out.println("update the seqPanel colours"); + // repaint(); + } + + public void mouseMoved(MouseEvent evt) + { + int res = findRes(evt); + int seq = findSeq(evt); + + if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0) + { + if (tooltip != null) + { + tooltip.setTip(""); + } + return; + } + + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + if (res > sequence.getLength()) + { + if (tooltip != null) + { + tooltip.setTip(""); + } + return; + } + + int respos = sequence.findPosition(res); + if (ssm != null) + mouseOverSequence(sequence, res, respos); + + 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 + " (" + respos + ")"); + } + } + + ap.alignFrame.statusBar.setText(text.toString()); + + StringBuffer tooltipText = new StringBuffer(); + SequenceGroup[] groups = av.alignment.findAllGroups(sequence); + if (groups != null) + { + for (int g = 0; g < groups.length; g++) + { + if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res) + { + if (!groups[g].getName().startsWith("JTreeGroup") + && !groups[g].getName().startsWith("JGroup")) + { + tooltipText.append(groups[g].getName() + " "); + } + if (groups[g].getDescription() != null) + { + tooltipText.append(groups[g].getDescription()); + } + tooltipText.append("\n"); + } + } + } + + // use aa to see if the mouse pointer is on a + SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, + sequence.findPosition(res)); + + int index = 0; + while (index < allFeatures.length) + { + SequenceFeature sf = allFeatures[index]; + + tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); + + if (sf.getDescription() != null) + { + tooltipText.append(" " + sf.getDescription()); + } + + if (sf.getValue("status") != null) + { + String status = sf.getValue("status").toString(); + if (status.length() > 0) + { + tooltipText.append(" (" + sf.getValue("status") + ")"); + } + } + tooltipText.append("\n"); + + index++; + } + + if (tooltip == null) + { + tooltip = new Tooltip(tooltipText.toString(), seqCanvas); + } + else + { + tooltip.setTip(tooltipText.toString()); + } + } + + SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) + { + Vector tmp = new Vector(); + SequenceFeature[] features = sequence.getSequenceFeatures(); + if (features != null) + { + for (int i = 0; i < features.length; i++) + { + if (av.featuresDisplayed == null + || !av.featuresDisplayed.containsKey(features[i].getType())) + { + continue; + } + + if (features[i].featureGroup != null + && seqCanvas.fr.featureGroups != null + && seqCanvas.fr.featureGroups + .containsKey(features[i].featureGroup) + && !((Boolean) seqCanvas.fr.featureGroups + .get(features[i].featureGroup)).booleanValue()) + continue; + + if ((features[i].getBegin() <= res) + && (features[i].getEnd() >= res)) + { + tmp.addElement(features[i]); + } + } + } + + features = new SequenceFeature[tmp.size()]; + tmp.copyInto(features); + + return features; + } + + Tooltip tooltip; + + public void mouseDragged(MouseEvent evt) + { + if (mouseWheelPressed) + { + int oldWidth = av.charWidth; + + // 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 (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++; + } + + 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.paintAlignment(false); + ap.annotationPanel.image = null; + return; + } + + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } + + int res = findRes(evt); + + if (res < 0) + { + res = 0; + } + + if ((lastres == -1) || (lastres == res)) + { + return; + } + + if ((res < av.getAlignment().getWidth()) && (res < lastres)) + { + // dragLeft, delete gap + editSequence(false, res); + } + else + { + editSequence(true, res); + } + + 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(); + + 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) + { + if (av.hiddenRepSequences == null + || !av.hiddenRepSequences.containsKey(seq)) + { + endEditing(); + return; + } + + 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 (fixedLeft < y1 && (fixedRight > y2 || 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 && startres < av.getColumnSelection() + .getHiddenBoundaryRight(startres))) + { + endEditing(); + return; + } + + int alWidth = av.alignment.getWidth(); + if (av.hasHiddenRows) + { + int hwidth = av.alignment.getHiddenSequences().getWidth(); + if (hwidth > alWidth) + { + 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.alignment, 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.alignment, 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.alignment, 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; m < lastres; m++) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) + { + break; + } + max++; + } + + if (max > 0) + { + editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] + { seq }, startres, max, av.alignment, true); + } + } + } + } + + lastres = startres; + seqCanvas.repaint(); + } + + void insertChar(int j, SequenceI[] seq, int fixedColumn) + { + int blankColumn = fixedColumn; + for (int s = 0; s < seq.length; s++) + { + // Find the next gap before the end of the visible region boundary + // If lastCol > j, theres a boundary after the gap insertion + + 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; + } + } + + if (blankColumn <= j) + { + blankColumn = fixedColumn; + endEditing(); + return; + } + } + + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, + av.alignment, true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment, + true); + + } + + void deleteChar(int j, SequenceI[] seq, int fixedColumn) + { + + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment, + true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, + av.alignment, true); + } + + // //////////////////////////////////////// + // ///Everything below this is for defining the boundary of the rubberband + // //////////////////////////////////////// + public void doMousePressedDefineMode(MouseEvent evt) + { + 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()) + { + return; + } + + stretchGroup = av.getSelectionGroup(); + + if (stretchGroup == null) + { + stretchGroup = av.alignment.findGroup(sequence); + if (stretchGroup != null && res > stretchGroup.getStartRes() + && res < stretchGroup.getEndRes()) + { + av.setSelectionGroup(stretchGroup); + } + else + { + stretchGroup = null; + } + } + + else if (!stretchGroup.getSequences(null).contains(sequence) + || stretchGroup.getStartRes() > res + || stretchGroup.getEndRes() < res) + { + stretchGroup = null; + + 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 + if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) + { + SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, + sequence.findPosition(res)); + + Vector links = null; + if (allFeatures != null) + { + for (int i = 0; i < allFeatures.length; i++) + { + if (allFeatures[i].links != null) + { + if (links == null) + { + links = new Vector(); + } + for (int j = 0; j < allFeatures[i].links.size(); j++) + { + links.addElement(allFeatures[i].links.elementAt(j)); + } + } + } + } + APopupMenu popup = new APopupMenu(ap, null, links); + this.add(popup); + popup.show(this, evt.getX(), evt.getY()); + return; + } + + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } + + // Only if left mouse button do we want to change group sizes + + 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"); + } + + } + } + + public void doMouseReleasedDefineMode(MouseEvent evt) + { + if (stretchGroup == null) + { + return; + } + + if (stretchGroup.cs != null) + { + if (stretchGroup.cs instanceof ClustalxColourScheme) + { + ((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.paintAlignment(true); + av.sendSelection(); + } + + public void doMouseDraggedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int y = findSeq(evt); + + if (wrappedBlock != startWrapBlock) + { + return; + } + + if (stretchGroup == null) + { + return; + } + + mouseDragging = true; + + if (y > av.alignment.getHeight()) + { + y = av.alignment.getHeight() - 1; + } + + if (res >= av.alignment.getWidth()) + { + res = av.alignment.getWidth() - 1; + } + + 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 (res < 0) + { + res = 0; + } + + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) + { + stretchGroup.setEndRes(res); + } + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) + { + stretchGroup.setStartRes(res); + } + } + + int dragDirection = 0; + + if (y > oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } + + 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); + + 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); + } + } + + if (oldSeq < 0) + { + oldSeq = -1; + } + + if (res > av.endRes || res < av.startRes || y < av.startSeq + || y > av.endSeq) + { + mouseExited(evt); + } + + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } + + seqCanvas.repaint(); + } + + public void mouseEntered(MouseEvent e) + { + if (oldSeq < 0) + { + oldSeq = 0; + } + + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } + } + + public void mouseExited(MouseEvent e) + { + if (av.getWrapAlignment()) + { + return; + } + + 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 + { + 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() >= getSize().height + && av.alignment.getHeight() > av.getEndSeq()) + { + running = ap.scrollUp(false); + } + + if (mouseDragging && evt.getX() < 0) + { + running = ap.scrollRight(false); + } + + else if (mouseDragging && evt.getX() >= getSize().width) + { + running = ap.scrollRight(true); + } + } + + try + { + Thread.sleep(75); + } catch (Exception ex) + { + } + } + } + } + + /** + * modify current selection according to a received message. + */ + public void selection(SequenceGroup seqsel, ColumnSelection colsel, + SelectionSource source) + { + // TODO: fix this hack - source of messages is align viewport, but SeqPanel + // handles selection messages... + // TODO: extend config options to allow user to control if selections may be + // shared between viewports. + if (av != null + && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source) + .getSequenceSetId().equals(av.getSequenceSetId())))) + { + return; + } + // do we want to thread this ? (contention with seqsel and colsel locks, I + // suspect) + // rules are: colsel is copied if there is a real intersection between + // sequence selection + boolean repaint = false, copycolsel = true; + if (av.selectionGroup == null || !av.isSelectionGroupChanged()) + { + SequenceGroup sgroup = null; + if (seqsel != null && seqsel.getSize()>0) + { + if (av.alignment == null) + { + System.out + .println("Selection message: alignviewport av SeqSetId=" + + av.getSequenceSetId() + " ViewId=" + + av.getViewId() + + " 's alignment is NULL! returning immediatly."); + return; + } + sgroup = seqsel.intersect(av.alignment, + (av.hasHiddenRows) ? av.hiddenRepSequences : null); + if ((sgroup == null || sgroup.getSize() == 0) + && (colsel == null || colsel.size() == 0)) + { + // don't copy columns if the region didn't intersect. + copycolsel = false; + } + } + if (sgroup != null && sgroup.getSize() > 0) + { + av.setSelectionGroup(sgroup); + } + else + { + av.setSelectionGroup(null); + } + repaint = av.isSelectionGroupChanged(); + } + if (copycolsel && (av.colSel == null || !av.isColSelChanged())) + { + // the current selection is unset or from a previous message + // so import the new colsel. + if (colsel == null || colsel.size() == 0) + { + if (av.colSel != null) + { + av.colSel.clear(); + } + } + else + { + // TODO: shift colSel according to the intersecting sequences + if (av.colSel == null) + { + av.colSel = new ColumnSelection(colsel); + } + else + { + av.colSel.setElementsFrom(colsel); + } + } + repaint |= av.isColSelChanged(); + } + if (copycolsel && av.hasHiddenColumns + && (av.colSel == null || av.colSel.getHiddenColumns() == null)) + { + System.err.println("Bad things"); + } + if (repaint) + { + ap.scalePanelHolder.repaint(); + ap.repaint(); + } + } + + /** + * scroll to the given row/column - or nearest visible location + * @param row + * @param column + */ + public void scrollTo(int row, int column) + { + + row = row<0 ? ap.av.startSeq : row; + column = column<0 ? ap.av.startRes : column; + ap.scrollTo(row, row, column, true, true); + } + /** + * scroll to the given row - or nearest visible location + * @param row + */ + public void scrollToRow(int row) + { + + row = row<0 ? ap.av.startSeq : row; + ap.scrollTo(row, row, ap.av.startRes, true, true); + } + /** + * scroll to the given column - or nearest visible location + * @param column + */ + public void scrollToColumn(int column) + { + + column = column<0 ? ap.av.startRes : column; + ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true); + } + +}