X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=89289c001d400292ad7c559ba86bcbcf03b64b9f;hb=4cea7a0328724b90a6a7c16ae8c926e0cc12cedd;hp=158f0abdbc98dc13589b0ae04a36c1625560440a;hpb=41e1e412121ed83380bd33fcb9e3969dc055aa4c;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java old mode 100755 new mode 100644 index 158f0ab..89289c0 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,22 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.*; @@ -27,47 +25,60 @@ 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 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 + // 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; @@ -80,7 +91,7 @@ public class SeqPanel seqCanvas.addMouseMotionListener(this); seqCanvas.addMouseListener(this); - ssm = StructureSelectionManager.getStructureSelectionManager(); + ssm = StructureSelectionManager.getStructureSelectionManager(av.applet); ssm.addStructureViewerListener(this); seqCanvas.repaint(); @@ -91,8 +102,8 @@ public class SeqPanel if (editCommand != null && editCommand.getSize() > 0) { ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, - av.getAlignment().getSequences()); + av.firePropertyChange("alignment", null, av.getAlignment() + .getSequences()); } startseq = -1; @@ -132,12 +143,10 @@ public class SeqPanel void setCursorPosition() { - SequenceI sequence = - (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( + seqCanvas.cursorY); - seqCanvas.cursorX = sequence.findIndex( - getKeyboardNo1() - 1 - ); + seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; scrollToVisible(); } @@ -145,20 +154,20 @@ public class SeqPanel { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; - if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() + && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; - int maxWidth = av.alignment.getWidth(); + int maxWidth = av.getAlignment().getWidth(); - while (!av.colSel.isVisible(seqCanvas.cursorX) - && seqCanvas.cursorX < maxWidth - && seqCanvas.cursorX > 0) + while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) + && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.colSel.isVisible(seqCanvas.cursorX)) + || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@ -172,18 +181,18 @@ public class SeqPanel { seqCanvas.cursorX = 0; } - else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) + else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1) { - seqCanvas.cursorX = av.alignment.getWidth() - 1; + seqCanvas.cursorX = av.getAlignment().getWidth() - 1; } if (seqCanvas.cursorY < 0) { seqCanvas.cursorY = 0; } - else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1) { - seqCanvas.cursorY = av.alignment.getHeight() - 1; + seqCanvas.cursorY = av.getAlignment().getHeight() - 1; } endEditing(); @@ -201,7 +210,8 @@ public class SeqPanel { ap.scrollUp(false); } - while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes)) + while (seqCanvas.cursorX < av.getColumnSelection() + .adjustForHiddenColumns(av.startRes)) { if (!ap.scrollRight(false)) @@ -209,7 +219,8 @@ public class SeqPanel break; } } - while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes)) + while (seqCanvas.cursorX > av.getColumnSelection() + .adjustForHiddenColumns(av.endRes)) { if (!ap.scrollRight(true)) { @@ -217,25 +228,25 @@ public class SeqPanel } } } - setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), - seqCanvas.cursorX, seqCanvas.cursorY); + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), + seqCanvas.cursorX, seqCanvas.cursorY); seqCanvas.repaint(); } void setSelectionAreaAtCursor(boolean topLeft) { - SequenceI sequence = - (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + 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; + SequenceGroup sg = av.getSelectionGroup(); + // Find the top and bottom of this group + int min = av.getAlignment().getHeight(), max = 0; for (int i = 0; i < sg.getSize(); i++) { - int index = av.alignment.findIndex(sg.getSequenceAt(i)); + int index = av.getAlignment().findIndex(sg.getSequenceAt(i)); if (index > max) { max = index; @@ -277,10 +288,10 @@ public class SeqPanel else { // Now add any sequences between min and max - sg.getSequences(null).removeAllElements(); + sg.clear(); for (int i = min; i < max; i++) { - sg.addSequence(av.alignment.getSequenceAt(i), false); + sg.addSequence(av.getAlignment().getSequenceAt(i), false); } } } @@ -293,8 +304,8 @@ public class SeqPanel sg.addSequence(sequence, false); av.setSelectionGroup(sg); } - ap.paintAlignment(false); + av.sendSelection(); } void insertGapAtCursor(boolean group) @@ -331,42 +342,45 @@ public class SeqPanel keyboardNo1.append(value); } } - int getKeyboardNo1() { - if (keyboardNo1 == null) - return 1; - else + try { + if (keyboardNo1 != null) { int value = Integer.parseInt(keyboardNo1.toString()); keyboardNo1 = null; return value; } + } catch (Exception x) + {} + keyboardNo1 = null; + return 1; } int getKeyboardNo2() { - if (keyboardNo2 == null) - return 1; - else - { + try { + if (keyboardNo2!=null){ int value = Integer.parseInt(keyboardNo2.toString()); keyboardNo2 = null; return value; } + } catch (Exception x) + {} + keyboardNo2 = null; + return 1; } - - + void setStatusMessage(SequenceI sequence, int res, int seq) { - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + - ""); + obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + + ""); if (obj != null) { text.append(" Nucleotide: "); @@ -386,8 +400,7 @@ public class SeqPanel if (obj != "") { - text.append(obj + " (" + sequence.findPosition(res) + - ")"); + text.append(obj + " (" + sequence.findPosition(res) + ")"); } } @@ -399,18 +412,16 @@ public class SeqPanel { 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) + // 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.isShiftDown() || evt.isControlDown() || evt.isAltDown()) { if (evt.isControlDown() || evt.isAltDown()) { @@ -432,8 +443,8 @@ public class SeqPanel return; } - if ( (seq < av.getAlignment().getHeight()) && - (res < av.getAlignment().getSequenceAt(seq).getLength())) + if ((seq < av.getAlignment().getHeight()) + && (res < av.getAlignment().getSequenceAt(seq).getLength())) { startseq = seq; lastres = res; @@ -449,34 +460,31 @@ public class SeqPanel public void mouseClicked(MouseEvent evt) { - SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt)); + SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); if (evt.getClickCount() > 1) { - if (av.getSelectionGroup().getSize() == 1 - && av.getSelectionGroup().getEndRes() - - av.getSelectionGroup().getStartRes() < 2) + if (av.getSelectionGroup() != null + && av.getSelectionGroup().getSize() == 1 + && av.getSelectionGroup().getEndRes() + - av.getSelectionGroup().getStartRes() < 2) { av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes( - sequence, - sequence.findPosition(findRes(evt)) - ); + 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()); + 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.getFeatureRenderer().amendFeatures(new SequenceI[] + { sequence }, features, false, ap); seqCanvas.highlightSearchResults(null); } @@ -500,7 +508,9 @@ public class SeqPanel } int startWrapBlock = -1; + int wrappedBlock = -1; + int findRes(MouseEvent evt) { int res = 0; @@ -515,8 +525,8 @@ public class SeqPanel hgap += av.charHeight; } - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + + seqCanvas.getAnnotationHeight(); int y = evt.getY(); y -= hgap; @@ -539,7 +549,7 @@ public class SeqPanel res = (x / av.getCharWidth()) + av.getStartRes(); } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } @@ -551,8 +561,9 @@ public class SeqPanel int findSeq(MouseEvent evt) { final int sqnum = findAlRow(evt); - return (sqnum<0) ? 0 : sqnum; + return (sqnum < 0) ? 0 : sqnum; } + /** * * @param evt @@ -571,13 +582,13 @@ public class SeqPanel hgap += av.charHeight; } - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + + seqCanvas.getAnnotationHeight(); y -= hgap; - seq = Math.min( (y % cHeight) / av.getCharHeight(), - av.alignment.getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() + .getHeight() - 1); if (seq < 0) { seq = -1; @@ -585,8 +596,8 @@ public class SeqPanel } else { - seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), - av.alignment.getHeight() - 1); + seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + .getAlignment().getHeight() - 1); if (seq < 0) { seq = -1; @@ -596,18 +607,16 @@ public class SeqPanel 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()) + if (seq < av.getAlignment().getHeight() + && res < av.getAlignment().getSequenceAt(seq).getLength()) { - //char resstr = align.getSequenceAt(seq).getSequence().charAt(res); + // char resstr = align.getSequenceAt(seq).getSequence().charAt(res); // Find the residue's position in the sequence (res is the position // in the alignment @@ -623,27 +632,34 @@ public class SeqPanel return; } - String lastMessage; + public void mouseOverSequence(SequenceI sequence, int index, int pos) { - String tmp = sequence.hashCode()+index+""; + String tmp = sequence.hashCode() + index + ""; if (lastMessage == null || !lastMessage.equals(tmp)) - ssm.mouseOverSequence(sequence, index, pos); + 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(); + // repaint(); } public void mouseMoved(MouseEvent evt) @@ -674,15 +690,14 @@ public class SeqPanel if (ssm != null) mouseOverSequence(sequence, res, respos); - - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + - ""); + obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + + ""); if (obj != null) { text.append(" Nucleotide: "); @@ -708,15 +723,15 @@ public class SeqPanel ap.alignFrame.statusBar.setText(text.toString()); StringBuffer tooltipText = new StringBuffer(); - SequenceGroup[] groups = av.alignment.findAllGroups(sequence); + SequenceGroup[] groups = av.getAlignment().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")) + if (!groups[g].getName().startsWith("JTreeGroup") + && !groups[g].getName().startsWith("JGroup")) { tooltipText.append(groups[g].getName() + " "); } @@ -730,33 +745,33 @@ public class SeqPanel } // use aa to see if the mouse pointer is on a - SequenceFeature [] allFeatures = findFeaturesAtRes(sequence, - sequence.findPosition(res)); + SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, + sequence.findPosition(res)); - int index = 0; - while (index < allFeatures.length) - { - SequenceFeature sf = allFeatures[index]; + int index = 0; + while (index < allFeatures.length) + { + SequenceFeature sf = allFeatures[index]; - tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); + tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); - if (sf.getDescription() != null) - { - tooltipText.append(" " + sf.getDescription()); - } + if (sf.getDescription() != null) + { + tooltipText.append(" " + sf.getDescription()); + } - if (sf.getValue("status") != null) + if (sf.getValue("status") != null) + { + String status = sf.getValue("status").toString(); + if (status.length() > 0) { - String status = sf.getValue("status").toString(); - if (status.length() > 0) - { - tooltipText.append(" (" + sf.getValue("status") + ")"); - } + tooltipText.append(" (" + sf.getValue("status") + ")"); } - tooltipText.append("\n"); - - index++; } + tooltipText.append("\n"); + + index++; + } if (tooltip == null) { @@ -777,22 +792,21 @@ public class SeqPanel for (int i = 0; i < features.length; i++) { if (av.featuresDisplayed == null - || !av.featuresDisplayed.containsKey(features[i].getType())) + || !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()) + && 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)) + if ((features[i].getBegin() <= res) + && (features[i].getEnd() >= res)) { tmp.addElement(features[i]); } @@ -805,7 +819,6 @@ public class SeqPanel return features; } - Tooltip tooltip; public void mouseDragged(MouseEvent evt) @@ -814,9 +827,9 @@ public class SeqPanel { 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)) + // 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(); @@ -879,12 +892,12 @@ public class SeqPanel res = 0; } - if ( (lastres == -1) || (lastres == res)) + if ((lastres == -1) || (lastres == res)) { return; } - if ( (res < av.getAlignment().getWidth()) && (res < lastres)) + if ((res < av.getAlignment().getWidth()) && (res < lastres)) { // dragLeft, delete gap editSequence(false, res); @@ -909,14 +922,13 @@ public class SeqPanel boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); - SequenceI seq = av.alignment.getSequenceAt(startseq); + SequenceI seq = av.getAlignment().getSequenceAt(startseq); - if (!groupEditing && av.hasHiddenRows) + if (!groupEditing && av.hasHiddenRows()) { - if (av.hiddenRepSequences != null - && av.hiddenRepSequences.containsKey(seq)) + if (av.isHiddenRepSequence(seq)) { - sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + sg = (SequenceGroup) av.getRepresentedSequences(seq); groupEditing = true; } } @@ -956,33 +968,33 @@ public class SeqPanel message.append(Math.abs(startres - lastres) + " gaps."); ap.alignFrame.statusBar.setText(message.toString()); - //Are we editing within a selection group? + // Are we editing within a selection group? if (groupEditing - || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq))) + || (sg != null && sg.getSequences(av.getHiddenRepSequences()) + .contains(seq))) { fixedColumns = true; - //sg might be null as the user may only see 1 sequence, - //but the sequence represents a group + // 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)) + if (!av.isHiddenRepSequence(seq)) { endEditing(); return; } - sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + sg = av.getRepresentedSequences(seq); } fixedLeft = sg.getStartRes(); fixedRight = sg.getEndRes(); - if ( (startres < fixedLeft && lastres >= fixedLeft) - || (startres >= fixedLeft && lastres < fixedLeft) - || (startres > fixedRight && lastres <= fixedRight) - || (startres <= fixedRight && lastres > fixedRight)) + if ((startres < fixedLeft && lastres >= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <= fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) { endEditing(); return; @@ -1000,21 +1012,21 @@ public class SeqPanel } } - if (av.hasHiddenColumns) + 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)) + 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 + // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + // Selection spans a hidden region if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) { if (startres >= y2) @@ -1030,25 +1042,18 @@ public class SeqPanel 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); - } + SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences()) + .toArray(new SequenceI[0]); // drag to right if (insertGap) { - //If the user has selected the whole sequence, and is dragging to + // 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 - ) + if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight + && sg.getEndRes() == av.getAlignment().getWidth() - 1) { - sg.setEndRes(av.alignment.getWidth() + startres - lastres); + sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); fixedRight = sg.getEndRes(); } @@ -1056,18 +1061,16 @@ public class SeqPanel // Find the next gap before the end // of the visible region boundary boolean blank = false; - for (fixedRight = fixedRight; - fixedRight > lastres; - fixedRight--) + for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--) { blank = true; - for (g = 0; g < groupSize; g++) + for (SequenceI gs : groupSeqs) { for (int j = 0; j < startres - lastres; j++) { - if (!jalview.util.Comparison.isGap( - groupSeqs[g].getCharAt(fixedRight - j))) + if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight + - j))) { blank = false; break; @@ -1082,27 +1085,27 @@ public class SeqPanel if (!blank) { - if (sg.getSize() == av.alignment.getHeight()) + if (sg.getSize() == av.getAlignment().getHeight()) { - if ( (av.hasHiddenColumns - && - startres < av.getColumnSelection().getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() && startres < av + .getColumnSelection().getHiddenBoundaryRight(startres))) { endEditing(); return; } - int alWidth = av.alignment.getWidth(); - if (av.hasHiddenRows) + int alWidth = av.getAlignment().getWidth(); + if (av.hasHiddenRows()) { - int hwidth = av.alignment.getHiddenSequences().getWidth(); + int hwidth = av.getAlignment().getHiddenSequences() + .getWidth(); if (hwidth > alWidth) { alWidth = hwidth; } } - //We can still insert gaps if the selectionGroup - //contains all the sequences + // We can still insert gaps if the selectionGroup + // contains all the sequences sg.setEndRes(sg.getEndRes() + startres - lastres); fixedRight = alWidth + startres - lastres; } @@ -1117,20 +1120,19 @@ public class SeqPanel // drag to left else if (!insertGap) { - /// Are we able to delete? + // / Are we able to delete? // ie are all columns blank? - for (g = 0; g < groupSize; g++) + for (SequenceI gs : groupSeqs) { for (int j = startres; j < lastres; j++) { - if (groupSeqs[g].getLength() <= j) + if (gs.getLength() <= j) { continue; } - if (!jalview.util.Comparison.isGap( - groupSeqs[g].getCharAt(j))) + if (!jalview.util.Comparison.isGap(gs.getCharAt(j))) { // Not a gap, block edit not valid endEditing(); @@ -1152,11 +1154,8 @@ public class SeqPanel } else { - editCommand.appendEdit(EditCommand.INSERT_GAP, - groupSeqs, - startres, startres - lastres, - av.alignment, - true); + editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs, + startres, startres - lastres, av.getAlignment(), true); } } else @@ -1171,16 +1170,14 @@ public class SeqPanel } else { - editCommand.appendEdit(EditCommand.DELETE_GAP, - groupSeqs, - startres, lastres - startres, - av.alignment, - true); + editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs, + startres, lastres - startres, av.getAlignment(), true); } } } - else /////Editing a single sequence/////////// + else + // ///Editing a single sequence/////////// { if (insertGap) { @@ -1190,17 +1187,13 @@ public class SeqPanel for (int j = lastres; j < startres; j++) { insertChar(j, new SequenceI[] - {seq}, fixedRight); + { seq }, fixedRight); } } else { - editCommand.appendEdit(EditCommand.INSERT_GAP, - new SequenceI[] - {seq}, - lastres, startres - lastres, - av.alignment, - true); + editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] + { seq }, lastres, startres - lastres, av.getAlignment(), true); } } else @@ -1216,12 +1209,12 @@ public class SeqPanel break; } deleteChar(startres, new SequenceI[] - {seq}, fixedRight); + { seq }, fixedRight); } } else { - //could be a keyboard edit trying to delete none gaps + // could be a keyboard edit trying to delete none gaps int max = 0; for (int m = startres; m < lastres; m++) { @@ -1234,12 +1227,8 @@ public class SeqPanel if (max > 0) { - editCommand.appendEdit(EditCommand.DELETE_GAP, - new SequenceI[] - {seq}, - startres, max, - av.alignment, - true); + editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] + { seq }, startres, max, av.getAlignment(), true); } } } @@ -1254,14 +1243,14 @@ public class SeqPanel 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 + // 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 + // Theres a space, so break and insert the gap break; } } @@ -1274,32 +1263,27 @@ public class SeqPanel } } - editCommand.appendEdit(EditCommand.DELETE_GAP, - seq, - blankColumn, 1, av.alignment, true); + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, - seq, - j, 1, av.alignment, - true); + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, + av.getAlignment(), true); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(EditCommand.DELETE_GAP, - seq, - j, 1, av.alignment, true); + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, - seq, - fixedColumn, 1, av.alignment, true); + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, + av.getAlignment(), true); } -////////////////////////////////////////// -/////Everything below this is for defining the boundary of the rubberband -////////////////////////////////////////// + // //////////////////////////////////////// + // ///Everything below this is for defining the boundary of the rubberband + // //////////////////////////////////////// public void doMousePressedDefineMode(MouseEvent evt) { if (scrollThread != null) @@ -1329,9 +1313,9 @@ public class SeqPanel if (stretchGroup == null) { - stretchGroup = av.alignment.findGroup(sequence); - if (stretchGroup != null && res > stretchGroup.getStartRes() && - res < stretchGroup.getEndRes()) + stretchGroup = av.getAlignment().findGroup(sequence); + if (stretchGroup != null && res > stretchGroup.getStartRes() + && res < stretchGroup.getEndRes()) { av.setSelectionGroup(stretchGroup); } @@ -1342,19 +1326,19 @@ public class SeqPanel } else if (!stretchGroup.getSequences(null).contains(sequence) - || stretchGroup.getStartRes() > res - || stretchGroup.getEndRes() < res) + || stretchGroup.getStartRes() > res + || stretchGroup.getEndRes() < res) { stretchGroup = null; - SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); if (allGroups != null) { for (int i = 0; i < allGroups.length; i++) { - if (allGroups[i].getStartRes() <= res && - allGroups[i].getEndRes() >= res) + if (allGroups[i].getStartRes() <= res + && allGroups[i].getEndRes() >= res) { stretchGroup = allGroups[i]; break; @@ -1365,11 +1349,10 @@ public class SeqPanel } // DETECT RIGHT MOUSE BUTTON IN AWT - if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) == - InputEvent.BUTTON3_MASK) + if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - SequenceFeature [] allFeatures = findFeaturesAtRes(sequence, - sequence.findPosition(res)); + SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, + sequence.findPosition(res)); Vector links = null; if (allFeatures != null) @@ -1378,7 +1361,10 @@ public class SeqPanel { if (allFeatures[i].links != null) { - links = new Vector(); + if (links == null) + { + links = new Vector(); + } for (int j = 0; j < allFeatures[i].links.size(); j++) { links.addElement(allFeatures[i].links.elementAt(j)); @@ -1400,7 +1386,7 @@ public class SeqPanel return; } - //Only if left mouse button do we want to change group sizes + // Only if left mouse button do we want to change group sizes if (stretchGroup == null) { @@ -1415,12 +1401,12 @@ public class SeqPanel if (av.getConservationSelected()) { SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), - "Background"); + "Background"); } if (av.getAbovePIDThreshold()) { SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); + "Background"); } } @@ -1433,33 +1419,22 @@ public class SeqPanel return; } + stretchGroup.recalcConservation(); // always do this - annotation has own + // state 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(); - } + stretchGroup.cs.alignmentChanged(stretchGroup, + av.getHiddenRepSequences()); if (stretchGroup.cs.conservationApplied()) { SliderPanel.setConservationSlider(ap, stretchGroup.cs, - stretchGroup.getName()); - stretchGroup.recalcConservation(); + stretchGroup.getName()); } else { SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); + stretchGroup.getName()); } } changeEndRes = false; @@ -1467,6 +1442,7 @@ public class SeqPanel stretchGroup = null; PaintRefresher.Refresh(ap, av.getSequenceSetId()); ap.paintAlignment(true); + av.sendSelection(); } public void doMouseDraggedDefineMode(MouseEvent evt) @@ -1486,14 +1462,14 @@ public class SeqPanel mouseDragging = true; - if (y > av.alignment.getHeight()) + if (y > av.getAlignment().getHeight()) { - y = av.alignment.getHeight() - 1; + y = av.getAlignment().getHeight() - 1; } - if (res >= av.alignment.getWidth()) + if (res >= av.getAlignment().getWidth()) { - res = av.alignment.getWidth() - 1; + res = av.getAlignment().getWidth() - 1; } if (stretchGroup.getEndRes() == res) @@ -1538,7 +1514,8 @@ public class SeqPanel dragDirection = -1; } - while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + while ((y != oldSeq) && (oldSeq > -1) + && (y < av.getAlignment().getHeight())) { // This routine ensures we don't skip any sequences, as the // selection is quite slow. @@ -1573,8 +1550,8 @@ public class SeqPanel oldSeq = -1; } - if (res > av.endRes || res < av.startRes - || y < av.startSeq || y > av.endSeq) + if (res > av.endRes || res < av.startRes || y < av.startSeq + || y > av.endSeq) { mouseExited(evt); } @@ -1639,11 +1616,12 @@ public class SeqPanel } // this class allows scrolling off the bottom of the visible alignment - class ScrollThread - extends Thread + class ScrollThread extends Thread { MouseEvent evt; + boolean running = false; + public ScrollThread() { start(); @@ -1673,8 +1651,8 @@ public class SeqPanel running = ap.scrollUp(true); } - if (mouseDragging && evt.getY() >= getSize().height && - av.alignment.getHeight() > av.getEndSeq()) + if (mouseDragging && evt.getY() >= getSize().height + && av.getAlignment().getHeight() > av.getEndSeq()) { running = ap.scrollUp(false); } @@ -1693,11 +1671,144 @@ public class SeqPanel try { Thread.sleep(75); + } catch (Exception ex) + { } - 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.getSelectionGroup() == null || !av.isSelectionGroupChanged(true)) + { + SequenceGroup sgroup = null; + if (seqsel != null && seqsel.getSize() > 0) + { + if (av.getAlignment() == 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.getAlignment(), + (av.hasHiddenRows()) ? av.getHiddenRepSequences() : 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(true); + } + if (copycolsel + && (av.getColumnSelection() == null || !av + .isColSelChanged(true))) + { + // the current selection is unset or from a previous message + // so import the new colsel. + if (colsel == null || colsel.size() == 0) + { + if (av.getColumnSelection() != null) + { + av.getColumnSelection().clear(); + } + } + else + { + // TODO: shift colSel according to the intersecting sequences + if (av.getColumnSelection() == null) + { + av.setColumnSelection(new ColumnSelection(colsel)); + } + else + { + av.getColumnSelection().setElementsFrom(colsel); + } + } + repaint |= av.isColSelChanged(true); + } + if (copycolsel + && av.hasHiddenColumns() + && (av.getColumnSelection() == null || av.getColumnSelection() + .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(column, column, row, 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(ap.av.startRes, ap.av.startRes, row, 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(column, column, ap.av.startSeq, true, true); + } + }