X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=8d81f8c49dceb3f114f13aa05e46b267c7b8ccba;hb=10866cba33b339de23e5a4e3121ab86c08b5ff2a;hp=ca5d7f7be2a2ba74bf6cddd90cc029cb0aeb28e9;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index ca5d7f7..8d81f8c 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,23 +1,24 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 + * 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 + * + * 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.gui; import java.util.*; +import java.util.List; import java.awt.*; import java.awt.event.*; @@ -26,12 +27,13 @@ import javax.swing.*; import jalview.commands.*; import jalview.datamodel.*; +import jalview.io.SequenceAnnotationReport; import jalview.schemes.*; import jalview.structure.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision: 1.130 $ */ @@ -86,7 +88,7 @@ public class SeqPanel extends JPanel implements MouseListener, StringBuffer keyboardNo2; java.net.URL linkImageURL; - + private final SequenceAnnotationReport seqARep; StringBuffer tooltipText = new StringBuffer(""); String tmpString; @@ -97,7 +99,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * Creates a new SeqPanel object. - * + * * @param avp * DOCUMENT ME! * @param p @@ -106,6 +108,7 @@ public class SeqPanel extends JPanel implements MouseListener, public SeqPanel(AlignViewport av, AlignmentPanel ap) { linkImageURL = getClass().getResource("/images/link.gif"); + seqARep=new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -176,7 +179,7 @@ public class SeqPanel extends JPanel implements MouseListener, res = (x / av.getCharWidth()) + av.getStartRes(); } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } @@ -204,12 +207,12 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; seq = Math.min((y % cHeight) / av.getCharHeight(), - av.alignment.getHeight() - 1); + av.getAlignment().getHeight() - 1); } else { seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), - av.alignment.getHeight() - 1); + av.getAlignment().getHeight() - 1); } return seq; @@ -297,7 +300,7 @@ public class SeqPanel extends JPanel implements MouseListener, void setCursorPosition() { - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( + SequenceI sequence = av.getAlignment().getSequenceAt( seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1); @@ -308,19 +311,19 @@ public class SeqPanel extends JPanel implements MouseListener, { 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) + 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; } @@ -335,18 +338,18 @@ public class SeqPanel extends JPanel implements MouseListener, { 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(); @@ -366,7 +369,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (!av.wrapAlignment) { - while (seqCanvas.cursorX < av.colSel + while (seqCanvas.cursorX < av.getColumnSelection() .adjustForHiddenColumns(av.startRes)) { if (!ap.scrollRight(false)) @@ -374,7 +377,7 @@ public class SeqPanel extends JPanel implements MouseListener, break; } } - while (seqCanvas.cursorX > av.colSel + while (seqCanvas.cursorX > av.getColumnSelection() .adjustForHiddenColumns(av.endRes)) { if (!ap.scrollRight(true)) @@ -384,7 +387,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } } - setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); seqCanvas.repaint(); @@ -392,17 +395,17 @@ public class SeqPanel extends JPanel implements MouseListener, void setSelectionAreaAtCursor(boolean topLeft) { - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( + SequenceI sequence = av.getAlignment().getSequenceAt( seqCanvas.cursorY); if (av.getSelectionGroup() != null) { - SequenceGroup sg = av.selectionGroup; + SequenceGroup sg = av.getSelectionGroup(); // Find the top and bottom of this group - int min = av.alignment.getHeight(), max = 0; + 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; @@ -447,7 +450,7 @@ public class SeqPanel extends JPanel implements MouseListener, sg.getSequences(null).clear(); for (int i = min; i < max; i++) { - sg.addSequence(av.alignment.getSequenceAt(i), false); + sg.addSequence(av.getAlignment().getSequenceAt(i), false); } } } @@ -470,7 +473,7 @@ public class SeqPanel extends JPanel implements MouseListener, groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; - editSequence(true, seqCanvas.cursorX + getKeyboardNo1()); + editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -479,10 +482,18 @@ public class SeqPanel extends JPanel implements MouseListener, groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX + getKeyboardNo1(); - editSequence(false, seqCanvas.cursorX); + editSequence(false, false, seqCanvas.cursorX); endEditing(); } + void insertNucAtCursor(boolean group,String nuc){ + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); + endEditing(); + } + void numberPressed(char value) { if (keyboardNo1 == null) @@ -526,10 +537,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { mouseDragging = false; @@ -546,10 +558,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); @@ -599,6 +612,7 @@ public class SeqPanel extends JPanel implements MouseListener, String lastMessage; + @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { String tmp = sequence.hashCode() + " " + index + " " + pos; @@ -611,6 +625,7 @@ public class SeqPanel extends JPanel implements MouseListener, lastMessage = tmp; } + @Override public void highlightSequence(SearchResults results) { if (av.followHighlight) @@ -623,6 +638,7 @@ public class SeqPanel extends JPanel implements MouseListener, seqCanvas.highlightSearchResults(results); } + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); @@ -631,10 +647,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent evt) { if (editingSeqs) @@ -665,7 +682,7 @@ public class SeqPanel extends JPanel implements MouseListener, tooltipText.setLength(6); // Cuts the buffer back to - SequenceGroup[] groups = av.alignment.findAllGroups(sequence); + SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) { for (int g = 0; g < groups.length; g++) @@ -698,7 +715,7 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceFeature[] features = findFeaturesAtRes( sequence.getDatasetSequence(), rpos = sequence.findPosition(res)); - appendFeatures(tooltipText, linkImageURL.toString(), rpos, features, + seqARep.appendFeatures(tooltipText, rpos, features, this.ap.seqPanel.seqCanvas.fr.minmax); } if (tooltipText.length() == 6) // @@ -744,151 +761,12 @@ public class SeqPanel extends JPanel implements MouseListener, return lastp = p; } - /** - * appends the features at rpos to the given stringbuffer ready for display in - * a tooltip - * - * @param tooltipText2 - * @param linkImageURL - * @param rpos - * @param features - * TODO refactor to Jalview 'utilities' somehow. - */ - public void appendFeatures(StringBuffer tooltipText2, - String linkImageURL, int rpos, SequenceFeature[] features) - { - appendFeatures(tooltipText2, linkImageURL, rpos, features, null); - } - - public void appendFeatures(StringBuffer tooltipText2, String string, - int rpos, SequenceFeature[] features, Hashtable minmax) - { - String tmpString; - if (features != null) - { - for (int i = 0; i < features.length; i++) - { - if (features[i].getType().equals("disulfide bond")) - { - if (features[i].getBegin() == rpos - || features[i].getEnd() == rpos) - { - if (tooltipText2.length() > 6) - { - tooltipText2.append("
"); - } - tooltipText2.append("disulfide bond " + features[i].getBegin() - + ":" + features[i].getEnd()); - if (features[i].links != null) - { - tooltipText2.append(" "); - } - } - } - else - { - if (tooltipText2.length() > 6) - { - tooltipText2.append("
"); - } - // TODO: remove this hack to display link only features - boolean linkOnly = features[i].getValue("linkonly") != null; - if (!linkOnly) - { - tooltipText2.append(features[i].getType() + " "); - if (rpos != 0) - { - // we are marking a positional feature - tooltipText2.append(features[i].begin); - } - if (features[i].begin != features[i].end) - { - tooltipText2.append(" " + features[i].end); - } - - if (features[i].getDescription() != null - && !features[i].description.equals(features[i] - .getType())) - { - tmpString = features[i].getDescription(); - String tmp2up=tmpString.toUpperCase(); - int startTag = tmp2up.indexOf(""); - if (startTag > -1) - { - tmpString = tmpString.substring(startTag + 6); - tmp2up = tmp2up.substring(startTag+6); - } - int endTag = tmp2up.indexOf(""); - if (endTag > -1) - { - tmpString = tmpString.substring(0, endTag); - tmp2up = tmp2up.substring(0, endTag); - } - endTag = tmp2up.indexOf(""); - if (endTag > -1) - { - tmpString = tmpString.substring(0, endTag); - } - - if (startTag > -1) - { - tooltipText2.append("; " + tmpString); - } - else - { - if (tmpString.indexOf("<") > -1 - || tmpString.indexOf(">") > -1) - { - // The description does not specify html is to - // be used, so we must remove < > symbols - tmpString = tmpString.replaceAll("<", "<"); - tmpString = tmpString.replaceAll(">", ">"); - - tooltipText2.append("; "); - tooltipText2.append(tmpString); - - } - else - { - tooltipText2.append("; " + tmpString); - } - } - } - // check score should be shown - if (features[i].getScore() != Float.NaN) - { - float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(features[i].getType())); - if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) - { - tooltipText2.append(" Score=" + features[i].getScore()); - } - } - if (features[i].getValue("status") != null) - { - String status = features[i].getValue("status").toString(); - if (status.length() > 0) - { - tooltipText2.append("; (" + features[i].getValue("status") - + ")"); - } - } - } - if (features[i].links != null) - { - tooltipText2.append(" "); - } - - } - } - } - } String lastTooltip; /** * Set status message in alignment panel - * + * * @param sequence * aligned sequence object * @param res @@ -904,7 +782,7 @@ public class SeqPanel extends JPanel implements MouseListener, + sequence.getName()); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + ""); @@ -936,10 +814,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) @@ -1013,11 +892,11 @@ public class SeqPanel extends JPanel implements MouseListener, if ((res < av.getAlignment().getWidth()) && (res < lastres)) { // dragLeft, delete gap - editSequence(false, res); + editSequence(false, false,res); } else { - editSequence(true, res); + editSequence(true, false,res); } mouseDragging = true; @@ -1027,22 +906,22 @@ public class SeqPanel extends JPanel implements MouseListener, } } - synchronized void editSequence(boolean insertGap, int startres) + //TODO: Make it more clever than many booleans + synchronized void editSequence(boolean insertGap, boolean editSeq, int startres) { int fixedLeft = -1; int fixedRight = -1; boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); - SequenceI seq = av.alignment.getSequenceAt(startseq); + SequenceI seq = av.getAlignment().getSequenceAt(startseq); // No group, but the sequence may represent a group - 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 = av.getRepresentedSequences(seq); groupEditing = true; } } @@ -1084,7 +963,7 @@ public class SeqPanel extends JPanel implements MouseListener, // Are we editing within a selection group? if (groupEditing - || (sg != null && sg.getSequences(av.hiddenRepSequences) + || (sg != null && sg.getSequences(av.getHiddenRepSequences()) .contains(seq))) { fixedColumns = true; @@ -1093,13 +972,12 @@ public class SeqPanel extends JPanel implements MouseListener, // 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(); @@ -1126,7 +1004,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { fixedColumns = true; int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); @@ -1156,12 +1034,12 @@ public class SeqPanel extends JPanel implements MouseListener, if (groupEditing) { - Vector vseqs = sg.getSequences(av.hiddenRepSequences); + List vseqs = sg.getSequences(av.getHiddenRepSequences()); int g, groupSize = vseqs.size(); SequenceI[] groupSeqs = new SequenceI[groupSize]; for (g = 0; g < groupSeqs.length; g++) { - groupSeqs[g] = (SequenceI) vseqs.elementAt(g); + groupSeqs[g] = vseqs.get(g); } // drag to right @@ -1170,9 +1048,9 @@ public class SeqPanel extends JPanel implements MouseListener, // 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.getEndRes() == av.getAlignment().getWidth() - 1) { - sg.setEndRes(av.alignment.getWidth() + startres - lastres); + sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); fixedRight = sg.getEndRes(); } @@ -1204,19 +1082,19 @@ public class SeqPanel extends JPanel implements MouseListener, if (!blank) { - if (sg.getSize() == av.alignment.getHeight()) + if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns && startres < av.getColumnSelection() + 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; @@ -1273,7 +1151,7 @@ public class SeqPanel extends JPanel implements MouseListener, else { editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.alignment, true); + startres, startres - lastres, av.getAlignment(), true); } } else @@ -1289,7 +1167,7 @@ public class SeqPanel extends JPanel implements MouseListener, else { editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.alignment, true); + startres, lastres - startres, av.getAlignment(), true); } } @@ -1311,11 +1189,12 @@ public class SeqPanel extends JPanel implements MouseListener, else { editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.alignment, true); - } + { seq }, lastres, startres - lastres, av.getAlignment(), true); + } } else { + if(!editSeq){ // dragging to the left if (fixedColumns && fixedRight != -1) { @@ -1346,9 +1225,24 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] - { seq }, startres, max, av.alignment, true); + { seq }, startres, max, av.getAlignment(), true); } } + }else{//insertGap==false AND editSeq==TRUE; + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, new SequenceI[] + { seq }, fixedRight); + } + } + else + { + editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[] + { seq }, lastres, startres - lastres, av.getAlignment(), true); + } + } } } @@ -1382,9 +1276,9 @@ public class SeqPanel extends JPanel implements MouseListener, } editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, - av.alignment, true); + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment, + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(), true); } @@ -1392,19 +1286,20 @@ public class SeqPanel extends JPanel implements MouseListener, void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment, + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(), true); editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, - av.alignment, true); + av.getAlignment(), true); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { if (oldSeq < 0) @@ -1421,10 +1316,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -1438,10 +1334,11 @@ public class SeqPanel extends JPanel implements MouseListener, } } + @Override public void mouseClicked(MouseEvent evt) { SequenceGroup sg = null; - SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt)); + SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); if (evt.getClickCount() > 1) { sg = av.getSelectionGroup(); @@ -1472,23 +1369,35 @@ public class SeqPanel extends JPanel implements MouseListener, } } + @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); if (e.getWheelRotation() > 0) { - ap.scrollUp(false); + if (e.isShiftDown()) + { + ap.scrollRight(true); + + } else { + ap.scrollUp(false); + } } else { - ap.scrollUp(true); + if (e.isShiftDown()) + { + ap.scrollRight(false); + } else { + ap.scrollUp(true); + } } // TODO Update tooltip for new position. } /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -1500,7 +1409,7 @@ public class SeqPanel extends JPanel implements MouseListener, startWrapBlock = wrappedBlock; - if (av.wrapAlignment && seq > av.alignment.getHeight()) + if (av.wrapAlignment && seq > av.getAlignment().getHeight()) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Cannot edit annotations in wrapped view.", @@ -1513,7 +1422,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) { @@ -1524,7 +1433,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup == null) { - stretchGroup = av.alignment.findGroup(sequence); + stretchGroup = av.getAlignment().findGroup(sequence); if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && (res < stretchGroup.getEndRes())) @@ -1542,7 +1451,7 @@ public class SeqPanel extends JPanel implements MouseListener, { stretchGroup = null; - SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); if (allGroups != null) { @@ -1633,7 +1542,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -1648,12 +1557,8 @@ public class SeqPanel extends JPanel implements MouseListener, // state if (stretchGroup.cs != null) { - if (stretchGroup.cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) stretchGroup.cs).resetClustalX( - stretchGroup.getSequences(av.hiddenRepSequences), - stretchGroup.getWidth()); - } + stretchGroup.cs.alignmentChanged( + stretchGroup,av.getHiddenRepSequences()); if (stretchGroup.cs.conservationApplied()) { @@ -1677,7 +1582,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt * DOCUMENT ME! */ @@ -1696,9 +1601,9 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - if (res >= av.alignment.getWidth()) + if (res >= av.getAlignment().getWidth()) { - res = av.alignment.getWidth() - 1; + res = av.getAlignment().getWidth() - 1; } if (stretchGroup.getEndRes() == res) @@ -1743,7 +1648,7 @@ public class SeqPanel extends JPanel implements MouseListener, 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. @@ -1834,6 +1739,7 @@ public class SeqPanel extends JPanel implements MouseListener, running = false; } + @Override public void run() { running = true; @@ -1848,7 +1754,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (mouseDragging && (evt.getY() >= getHeight()) - && (av.alignment.getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getEndSeq())) { running = ap.scrollUp(false); } @@ -1876,6 +1782,7 @@ public class SeqPanel extends JPanel implements MouseListener, /** * modify current selection according to a received message. */ + @Override public void selection(SequenceGroup seqsel, ColumnSelection colsel, SelectionSource source) { @@ -1901,15 +1808,15 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceGroup sgroup = null; if (seqsel != null && seqsel.getSize()>0) { - if (av.alignment == null) + if (av.getAlignment() == null) { jalview.bin.Cache.log.warn("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); + sgroup = seqsel.intersect(av.getAlignment(), + (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); if ((sgroup == null || sgroup.getSize() == 0) || (colsel == null || colsel.size() == 0)) { @@ -1934,29 +1841,29 @@ public class SeqPanel extends JPanel implements MouseListener, // so import the new colsel. if (colsel == null || colsel.size() == 0) { - if (av.colSel != null) + if (av.getColumnSelection() != null) { - av.colSel.clear(); + av.getColumnSelection().clear(); repaint=true; } } else { // TODO: shift colSel according to the intersecting sequences - if (av.colSel == null) + if (av.getColumnSelection() == null) { - av.colSel = new ColumnSelection(colsel); + av.setColumnSelection(new ColumnSelection(colsel)); } else { - av.colSel.setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel); } } av.isColSelChanged(true); repaint = true; } - if (copycolsel && av.hasHiddenColumns - && (av.colSel == null || av.colSel.getHiddenColumns() == null)) + if (copycolsel && av.hasHiddenColumns() + && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null)) { System.err.println("Bad things"); }