X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1cc87156c7a93ba356bd31c29d6df1c27f9a0b3b;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=a1913a85af1850d7ddb18e97f3d8101d6a33fd04;hpb=ef2f3ba1a36fe7512e80bc1a3ce92d689f40b358;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java old mode 100755 new mode 100644 index a1913a8..1cc8715 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,39 +1,63 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.structure.*; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SearchResults; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.SequenceAnnotationReport; +import jalview.schemes.ResidueProperties; +import jalview.structure.SelectionListener; +import jalview.structure.SelectionSource; +import jalview.structure.SequenceListener; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Point; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.MouseWheelEvent; +import java.awt.event.MouseWheelListener; +import java.util.List; +import java.util.Vector; + +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.ToolTipManager; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.130 $ */ public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener, SequenceListener, @@ -87,7 +111,9 @@ public class SeqPanel extends JPanel implements MouseListener, java.net.URL linkImageURL; - StringBuffer tooltipText = new StringBuffer(""); + private final SequenceAnnotationReport seqARep; + + StringBuffer tooltipText = new StringBuffer(); String tmpString; @@ -106,6 +132,7 @@ 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); @@ -123,7 +150,7 @@ public class SeqPanel extends JPanel implements MouseListener, addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = StructureSelectionManager.getStructureSelectionManager(); + ssm = av.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@ -168,15 +195,16 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - if (x>seqCanvas.getWidth()+seqCanvas.getWidth()) + if (x > seqCanvas.getWidth() + seqCanvas.getWidth()) { - // make sure we calculate relative to visible alignment, rather than right-hand gutter - x = seqCanvas.getX()+seqCanvas.getWidth(); + // make sure we calculate relative to visible alignment, rather than + // right-hand gutter + x = seqCanvas.getX() + seqCanvas.getWidth(); } res = (x / av.getCharWidth()) + av.getStartRes(); } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } @@ -203,54 +231,18 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), - av.alignment.getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() + .getHeight() - 1); } 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); } return seq; } - 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; - } - void endEditing() { if (editCommand != null && editCommand.getSize() > 0) @@ -297,10 +289,9 @@ public class SeqPanel extends JPanel implements MouseListener, void setCursorPosition() { - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( - seqCanvas.cursorY); + SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); - seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1); + seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; scrollToVisible(); } @@ -308,19 +299,20 @@ 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 +327,18 @@ 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 +358,7 @@ 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 +366,7 @@ 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 +376,7 @@ 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 +384,16 @@ public class SeqPanel extends JPanel implements MouseListener, void setSelectionAreaAtCursor(boolean topLeft) { - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( - seqCanvas.cursorY); + 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 +438,7 @@ 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 +461,7 @@ 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(); } @@ -479,7 +470,16 @@ 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(); } @@ -502,26 +502,36 @@ public class SeqPanel extends JPanel implements MouseListener, 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) { - int value = Integer.parseInt(keyboardNo1.toString()); - keyboardNo1 = null; - return value; } + 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) { - int value = Integer.parseInt(keyboardNo2.toString()); - keyboardNo2 = null; - return value; } + keyboardNo2 = null; + return 1; } /** @@ -530,6 +540,7 @@ public class SeqPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { mouseDragging = false; @@ -550,6 +561,7 @@ public class SeqPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); @@ -599,6 +611,7 @@ 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; @@ -611,18 +624,20 @@ public class SeqPanel extends JPanel implements MouseListener, lastMessage = tmp; } + @Override public void highlightSequence(SearchResults results) { if (av.followHighlight) { if (ap.scrollToPosition(results, false)) { - seqCanvas.revalidate(); + seqCanvas.revalidate(); } } seqCanvas.highlightSearchResults(results); } + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); @@ -635,6 +650,7 @@ public class SeqPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent evt) { if (editingSeqs) @@ -661,22 +677,19 @@ public class SeqPanel extends JPanel implements MouseListener, pos = setStatusMessage(sequence, res, seq); if (ssm != null && pos > -1) + { mouseOverSequence(sequence, res, pos); + } 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++) { if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res) { - if (tooltipText.length() > 6) - { - tooltipText.append("
"); - } - if (!groups[g].getName().startsWith("JTreeGroup") && !groups[g].getName().startsWith("JGroup")) { @@ -692,14 +705,14 @@ public class SeqPanel extends JPanel implements MouseListener, } // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { int rpos; - SequenceFeature[] features = findFeaturesAtRes( + List features = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), rpos = sequence.findPosition(res)); - appendFeatures(tooltipText, linkImageURL.toString(), rpos, features, - this.ap.seqPanel.seqCanvas.fr.minmax); + seqARep.appendFeatures(tooltipText, rpos, features, + this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } if (tooltipText.length() == 6) // { @@ -708,11 +721,13 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - tooltipText.append(""); if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString())) { - setToolTipText(tooltipText.toString()); + String formatedTooltipText = JvSwingUtils.wrapTooltip(true, + tooltipText.toString()); + // String formatedTooltipText = tooltipText.toString(); + setToolTipText(formatedTooltipText); lastTooltip = tooltipText.toString(); } @@ -744,143 +759,6 @@ 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(); - int startTag = tmpString.toUpperCase().indexOf(""); - if (startTag > -1) - { - tmpString = tmpString.substring(startTag + 6); - } - int endTag = tmpString.toUpperCase().indexOf(""); - if (endTag > -1) - { - tmpString = tmpString.substring(0, endTag); - } - endTag = tmpString.toUpperCase().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; /** @@ -901,7 +779,7 @@ 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) + ""); @@ -937,6 +815,7 @@ public class SeqPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) @@ -1010,11 +889,11 @@ 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; @@ -1024,22 +903,23 @@ 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; } } @@ -1050,7 +930,7 @@ public class SeqPanel extends JPanel implements MouseListener, message.append("Edit group:"); if (editCommand == null) { - editCommand = new EditCommand("Edit Group"); + editCommand = new EditCommand(MessageManager.getString("action.edit_group")); } } else @@ -1063,7 +943,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (editCommand == null) { - editCommand = new EditCommand("Edit " + label); + editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); } } @@ -1081,7 +961,7 @@ 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; @@ -1090,13 +970,12 @@ 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(); @@ -1123,7 +1002,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { fixedColumns = true; int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); @@ -1153,12 +1032,12 @@ 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 @@ -1167,9 +1046,9 @@ 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(); } @@ -1201,19 +1080,20 @@ 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() - .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; @@ -1269,8 +1149,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.alignment, true); + editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, + startres, startres - lastres, av.getAlignment(), true); } } else @@ -1285,8 +1165,8 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.alignment, true); + editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, + startres, lastres - startres, av.getAlignment(), true); } } @@ -1307,43 +1187,63 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.alignment, true); + editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] + { seq }, lastres, startres - lastres, av.getAlignment(), true); } } else { - // dragging to the left - if (fixedColumns && fixedRight != -1) + if (!editSeq) { - for (int j = lastres; j > startres; j--) + // dragging to the left + if (fixedColumns && fixedRight != -1) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + for (int j = lastres; j > startres; j--) { - endEditing(); - break; + 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(Action.DELETE_GAP, + new SequenceI[] + { seq }, startres, max, av.getAlignment(), true); } - 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++) + {// insertGap==false AND editSeq==TRUE; + if (fixedColumns && fixedRight != -1) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) + for (int j = lastres; j < startres; j++) { - break; + insertChar(j, new SequenceI[] + { seq }, fixedRight); } - max++; } - - if (max > 0) + else { - editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] - { seq }, startres, max, av.alignment, true); + editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[] + { seq }, lastres, startres - lastres, av.getAlignment(), true); } } } @@ -1378,22 +1278,22 @@ public class SeqPanel extends JPanel implements MouseListener, } } - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, - av.alignment, true); + editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment, - true); + editCommand.appendEdit(Action.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(Action.DELETE_GAP, seq, j, 1, + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, - av.alignment, true); + editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1, + av.getAlignment(), true); } /** @@ -1402,6 +1302,7 @@ public class SeqPanel extends JPanel implements MouseListener, * @param e * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { if (oldSeq < 0) @@ -1422,6 +1323,7 @@ public class SeqPanel extends JPanel implements MouseListener, * @param e * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -1435,10 +1337,11 @@ 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(); @@ -1448,37 +1351,53 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes( + List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), + features.get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); } - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features, false, ap); + { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap); seqCanvas.highlightSearchResults(null); } } } + @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. } @@ -1497,11 +1416,12 @@ 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.", - "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("label.cannot_edit_annotations_in_wrapped_view"), + MessageManager.getString("label.wrapped_view_no_edit"), + JOptionPane.WARNING_MESSAGE); return; } @@ -1510,7 +1430,7 @@ 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())) { @@ -1521,7 +1441,7 @@ 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())) @@ -1539,7 +1459,7 @@ public class SeqPanel extends JPanel implements MouseListener, { stretchGroup = null; - SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); if (allGroups != null) { @@ -1560,16 +1480,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - SequenceFeature[] allFeatures = findFeaturesAtRes( + List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(res)); Vector links = new Vector(); - for (int i = 0; i < allFeatures.length; i++) + for (SequenceFeature sf:allFeatures) { - if (allFeatures[i].links != null) + if (sf.links != null) { - for (int j = 0; j < allFeatures[i].links.size(); j++) + for (int j = 0; j < sf.links.size(); j++) { - links.addElement(allFeatures[i].links.elementAt(j)); + links.addElement(sf.links.elementAt(j)); } } } @@ -1645,12 +1565,8 @@ 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()) { @@ -1693,9 +1609,9 @@ 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) @@ -1740,7 +1656,8 @@ 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. @@ -1831,6 +1748,7 @@ public class SeqPanel extends JPanel implements MouseListener, running = false; } + @Override public void run() { running = true; @@ -1845,7 +1763,7 @@ 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); } @@ -1873,6 +1791,7 @@ 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) { @@ -1882,7 +1801,8 @@ public class SeqPanel extends JPanel implements MouseListener, // shared between viewports. if (av == source || !av.followSelection - || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) + || (av.isSelectionGroupChanged(false) || av + .isColSelChanged(false)) || (source instanceof AlignViewport && ((AlignViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))) { @@ -1896,17 +1816,17 @@ public class SeqPanel extends JPanel implements MouseListener, // if (!av.isSelectionGroupChanged(false)) { SequenceGroup sgroup = null; - if (seqsel != null && seqsel.getSize()>0) + 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)) { @@ -1931,29 +1851,31 @@ 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(); - repaint=true; + 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"); }