X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=a20165a78123a2ffbe1ba0d85225a08d37e50f95;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=8de1d014b46a3e412a7b210c8e2040f2b062f14b;hpb=410dfa093c4150aeadc02710c2a70eb862e3b2d8;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 8de1d01..a20165a 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -18,15 +18,15 @@ */ package jalview.gui; -import jalview.datamodel.*; -import jalview.commands.EditCommand; -import jalview.schemes.*; +import java.util.*; import java.awt.*; import java.awt.event.*; import javax.swing.*; -import java.util.Vector; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.schemes.*; /** * DOCUMENT ME! @@ -34,7 +34,8 @@ import java.util.Vector; * @author $author$ * @version $Revision$ */ -public class SeqPanel extends JPanel implements MouseListener, +public class SeqPanel + extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener { @@ -116,7 +117,9 @@ public class SeqPanel extends JPanel implements MouseListener, int hgap = av.charHeight; if (av.scaleAboveWrapped) + { hgap += av.charHeight; + } int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + seqCanvas.getAnnotationHeight(); @@ -127,7 +130,9 @@ public class SeqPanel extends JPanel implements MouseListener, int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) + { return 0; + } wrappedBlock = y / cHeight; wrappedBlock += av.getStartRes() / cwidth; @@ -141,7 +146,9 @@ public class SeqPanel extends JPanel implements MouseListener, } if (av.hasHiddenColumns) + { res = av.getColumnSelection().adjustForHiddenColumns(res); + } return res; @@ -156,7 +163,9 @@ public class SeqPanel extends JPanel implements MouseListener, { int hgap = av.charHeight; if (av.scaleAboveWrapped) + { hgap += av.charHeight; + } int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + seqCanvas.getAnnotationHeight(); @@ -185,7 +194,9 @@ public class SeqPanel extends JPanel implements MouseListener, { if (av.featuresDisplayed == null || !av.featuresDisplayed.containsKey(features[i].getType())) + { continue; + } if ( (features[i].getBegin() <= res) && (features[i].getEnd() >= res)) @@ -196,1463 +207,1572 @@ public class SeqPanel extends JPanel implements MouseListener, } features = new SequenceFeature[tmp.size()]; - for(int i=0; i= res) - { - if (av.featuresDisplayed.containsKey(sf.getType())) - { - allFeatures.addElement(sf); - } - } - index++; - } - } - return allFeatures; + Vector getAllFeaturesAtRes(SequenceI seq, int res) + { + Vector allFeatures = new Vector(); + int index = 0; + if (seq.getSequenceFeatures() != null && av.featuresDisplayed != null) + { + while (index < seq.getSequenceFeatures().length) + { + SequenceFeature sf = seq.getSequenceFeatures()[index]; + if (sf.getBegin() <= res && + sf.getEnd() >= res) + { + if (av.featuresDisplayed.containsKey(sf.getType())) + { + allFeatures.addElement(sf); + } + } + index++; + } + } + return allFeatures; } - void endEditing() - { - if (editCommand!=null && editCommand.getSize() > 0) - { - ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, - av.getAlignment().getSequences()); - } - - startseq = -1; - lastres = -1; - editingSeqs = false; - groupEditing = false; - keyboardNo1 = null; - keyboardNo2 = null; - editCommand = null; + void endEditing() + { + if (editCommand != null && editCommand.getSize() > 0) + { + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); } - void setCursorRow() + startseq = -1; + lastres = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = null; + } + + void setCursorRow() + { + seqCanvas.cursorY = getKeyboardNo(keyboardNo1) - 1; + scrollToVisible(); + } + + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; + scrollToVisible(); + } + + void setCursorRowAndColumn() + { + if (keyboardNo2 == null) { - seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; - scrollToVisible(); + keyboardNo2 = new StringBuffer(); } - - void setCursorColumn() + else { - seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; + seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; + seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; scrollToVisible(); } + } + + void setCursorPosition() + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + + seqCanvas.cursorX = sequence.findIndex( + getKeyboardNo(keyboardNo1) - 1 + ); + scrollToVisible(); + } - void setCursorRowAndColumn() + void moveCursor(int dx, int dy) + { + seqCanvas.cursorX += dx; + seqCanvas.cursorY += dy; + if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) { - if(keyboardNo2==null) + int original = seqCanvas.cursorX - dx; + int maxWidth = av.alignment.getWidth(); + + while (!av.colSel.isVisible(seqCanvas.cursorX) + && seqCanvas.cursorX < maxWidth + && seqCanvas.cursorX > 0) { - keyboardNo2 = new StringBuffer(); + seqCanvas.cursorX += dx; } - else + + if (seqCanvas.cursorX >= maxWidth + || !av.colSel.isVisible(seqCanvas.cursorX)) { - seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; - seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; - scrollToVisible(); + seqCanvas.cursorX = original; } } - void setCursorPosition() + scrollToVisible(); + } + + void scrollToVisible() + { + if (seqCanvas.cursorX < 0) + { + seqCanvas.cursorX = 0; + } + else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) { - SequenceI sequence = - (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + seqCanvas.cursorX = av.alignment.getWidth() - 1; + } - seqCanvas.cursorX = sequence.findIndex( - getKeyboardNo(keyboardNo1)-1 - ); - scrollToVisible(); + if (seqCanvas.cursorY < 0) + { + seqCanvas.cursorY = 0; + } + else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + { + seqCanvas.cursorY = av.alignment.getHeight() - 1; } - void moveCursor(int dx, int dy) + endEditing(); + if (av.wrapAlignment) + { + ap.scrollToWrappedVisible(seqCanvas.cursorX); + } + else { - seqCanvas.cursorX += dx; - seqCanvas.cursorY += dy; - if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) + while (seqCanvas.cursorY < av.startSeq) { - int original = seqCanvas.cursorX - dx; - int maxWidth = av.alignment.getWidth(); - - while(!av.colSel.isVisible(seqCanvas.cursorX) - && seqCanvas.cursorX0) + ap.scrollUp(true); + } + while (seqCanvas.cursorY + 1 > av.endSeq) + { + ap.scrollUp(false); + } + if (!av.wrapAlignment) + { + while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes)) { - seqCanvas.cursorX += dx; + if (!ap.scrollRight(false)) + { + break; + } } - - if(seqCanvas.cursorX>=maxWidth - || !av.colSel.isVisible(seqCanvas.cursorX) ) + while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes)) { - seqCanvas.cursorX = original; + if (!ap.scrollRight(true)) + { + break; + } } } - - scrollToVisible(); } + setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + seqCanvas.cursorX, seqCanvas.cursorY); - void scrollToVisible() - { - if (seqCanvas.cursorX < 0) - seqCanvas.cursorX = 0; - else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) - seqCanvas.cursorX = av.alignment.getWidth() - 1; - - if (seqCanvas.cursorY < 0) - seqCanvas.cursorY = 0; - else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) - seqCanvas.cursorY = av.alignment.getHeight() - 1; + seqCanvas.repaint(); + } + void setSelectionAreaAtCursor(boolean topLeft) + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); - endEditing(); - if(av.wrapAlignment) - { - ap.scrollToWrappedVisible(seqCanvas.cursorX); - } - else + if (av.getSelectionGroup() != null) + { + SequenceGroup sg = av.selectionGroup; + //Find the top and bottom of this group + int min = av.alignment.getHeight(), max = 0; + for (int i = 0; i < sg.getSize(); i++) { - while (seqCanvas.cursorY < av.startSeq) + int index = av.alignment.findIndex(sg.getSequenceAt(i)); + if (index > max) { - ap.scrollUp(true); + max = index; } - while (seqCanvas.cursorY + 1 > av.endSeq) + if (index < min) { - ap.scrollUp(false); - } - if (!av.wrapAlignment) - { - while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes)) - { - if (!ap.scrollRight(false)) - break; - } - while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes)) - { - if (!ap.scrollRight(true)) - break; - } + min = index; } } - setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), - seqCanvas.cursorX, seqCanvas.cursorY); - seqCanvas.repaint(); - } - - void setSelectionAreaAtCursor(boolean topLeft) - { - SequenceI sequence = - (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + max++; - if(av.getSelectionGroup()!=null) + if (topLeft) { - SequenceGroup sg = av.selectionGroup; - //Find the top and bottom of this group - int min = av.alignment.getHeight(), max = 0; - for(int i=0; i max) - max = index; - if(index < min) - min = index; + sg.setEndRes(seqCanvas.cursorX); } - max ++; - - if(topLeft) + min = seqCanvas.cursorY; + } + else + { + sg.setEndRes(seqCanvas.cursorX); + if (sg.getStartRes() > seqCanvas.cursorX) { sg.setStartRes(seqCanvas.cursorX); - if(sg.getEndRes()seqCanvas.cursorX) - sg.setStartRes(seqCanvas.cursorX); - max = seqCanvas.cursorY+1; - } + max = seqCanvas.cursorY + 1; + } - if(min>max) - { - // Only the user can do this - av.setSelectionGroup(null); - } - else + if (min > max) + { + // Only the user can do this + av.setSelectionGroup(null); + } + else + { + // Now add any sequences between min and max + sg.getSequences(null).clear(); + for (int i = min; i < max; i++) { - // Now add any sequences between min and max - sg.getSequences(null).clear(); - for (int i = min; i < max; i++) - { - sg.addSequence(av.alignment.getSequenceAt(i), false); - } + sg.addSequence(av.alignment.getSequenceAt(i), false); } } + } - if (av.getSelectionGroup() == null) - { - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(seqCanvas.cursorX); - sg.setEndRes(seqCanvas.cursorX); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - } + if (av.getSelectionGroup() == null) + { + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(seqCanvas.cursorX); + sg.setEndRes(seqCanvas.cursorX); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + } + ap.repaint(); + } - ap.repaint(); - } + void insertGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX + getKeyboardNo(keyboardNo1)); + endEditing(); + } + + void deleteGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX + getKeyboardNo(keyboardNo1); + editSequence(false, seqCanvas.cursorX); + endEditing(); + } - void insertGapAtCursor(boolean group) + void numberPressed(char value) + { + if (keyboardNo1 == null) { - groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; - editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); - endEditing(); + keyboardNo1 = new StringBuffer(); } - void deleteGapAtCursor(boolean group) + if (keyboardNo2 != null) { - groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); - editSequence(false, seqCanvas.cursorX); - endEditing(); + keyboardNo2.append(value); } - - void numberPressed(char value) + else { - if(keyboardNo1==null) - keyboardNo1 = new StringBuffer(); - - if(keyboardNo2!=null) - keyboardNo2.append(value); - else - keyboardNo1.append(value); + keyboardNo1.append(value); } + } - int getKeyboardNo(StringBuffer kb) + int getKeyboardNo(StringBuffer kb) + { + if (kb == null) { - if(kb==null) - return 1; - else - return Integer.parseInt(kb.toString()); + return 1; } - - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) + else { - mouseDragging = false; - mouseWheelPressed = false; - - if (!editingSeqs) - { - doMouseReleasedDefineMode(evt); - return; - } + return Integer.parseInt(kb.toString()); + } + } - endEditing(); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseReleased(MouseEvent evt) + { + mouseDragging = false; + mouseWheelPressed = false; - ap.repaint(); + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; } + endEditing(); + + ap.repaint(); + } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mousePressed(MouseEvent evt) + { + lastMousePress = evt.getPoint(); - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mousePressed(MouseEvent evt) + if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) { - lastMousePress = evt.getPoint(); + mouseWheelPressed = true; + return; + } - if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + if (evt.isShiftDown() || evt.isAltDown() || + evt.isControlDown()) + { + if (evt.isAltDown() || evt.isControlDown()) { - mouseWheelPressed = true; - return; + groupEditing = true; } + editingSeqs = true; + } + else + { + doMousePressedDefineMode(evt); + return; + } - if (evt.isShiftDown() || evt.isAltDown() || - evt.isControlDown()) - { - if (evt.isAltDown() || evt.isControlDown()) - { - groupEditing = true; - } - editingSeqs = true; - } - else - { - doMousePressedDefineMode(evt); - return; - } + int seq = findSeq(evt); + int res = findRes(evt); - int seq = findSeq(evt); - int res = findRes(evt); + if (seq < 0 || res < 0) + { + return; + } - if(seq<0 || res<0) - return; + if ( (seq < av.getAlignment().getHeight()) && + (res < av.getAlignment().getSequenceAt(seq).getLength())) + { + startseq = seq; + lastres = res; + } + else + { + startseq = -1; + lastres = -1; + } - if ((seq < av.getAlignment().getHeight()) && - (res < av.getAlignment().getSequenceAt(seq).getLength())) - { - startseq = seq; - lastres = res; - } - else - { - startseq = -1; - lastres = -1; - } + return; + } - return; + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseMoved(MouseEvent evt) + { + if (editingSeqs) + { + // This is because MacOSX creates a mouseMoved + // If control is down, other platforms will not. + mouseDragged(evt); } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseMoved(MouseEvent evt) + int res = findRes(evt); + int seq = findSeq(evt); + + if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { - if (editingSeqs) - { - // This is because MacOSX creates a mouseMoved - // If control is down, other platforms will not. - mouseDragged(evt); - } + return; + } - int res = findRes(evt); - int seq = findSeq(evt); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + if (res > sequence.getLength()) + { + return; + } - if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) - return; + if (seqCanvas.pdbCanvas != null && sequence == seqCanvas.pdbCanvas.sequence) + { + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + } - SequenceI sequence = av.getAlignment().getSequenceAt(seq); + setStatusMessage(sequence, res, seq); - if (res > sequence.getLength()) - { - return; - } + tooltipText.setLength(6); // Cuts the buffer back to - if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) + SequenceGroup[] groups = av.alignment.findAllGroups(sequence); + if (groups != null) + { + for (int g = 0; g < groups.length; g++) { - seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + 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")) + { + tooltipText.append(groups[g].getName()); + } + + if (groups[g].getDescription() != null) + { + tooltipText.append(": " + groups[g].getDescription()); + } + } } + } - setStatusMessage(sequence, res, seq); + // use aa to see if the mouse pointer is on a + if (av.showSequenceFeatures) + { + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), sequence.findPosition(res)); - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) + if (features != null) + { + for (int i = 0; i < features.length; i++) { - tooltipText.setLength(6); // Cuts the buffer back to + if (features[i].getType().equals("disulfide bond")) + { + if (features[i].getBegin() == sequence.findPosition(res) + || features[i].getEnd() == sequence.findPosition(res)) + { + if (tooltipText.length() > 6) + { + tooltipText.append("
"); + } + tooltipText.append("disulfide bond " + features[i].getBegin() + + ":" + + features[i].getEnd()); + if (features[i].links != null) + { + tooltipText.append(" "); + } + } + } + else + { + if (tooltipText.length() > 6) + { + tooltipText.append("
"); + } - SequenceFeature[] features = findFeaturesAtRes( - sequence.getDatasetSequence(), sequence.findPosition(res)); + tooltipText.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + { + tooltipText.append(" " + features[i].end); + } - if(features!=null) + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) { - for (int i = 0; i < features.length; i++) + tmpString = features[i].getDescription(); + int startTag = tmpString.toUpperCase().indexOf(""); + if (startTag > -1) { - if (features[i].getType().equals("disulfide bond")) - { - if (features[i].getBegin() == sequence.findPosition(res) - || features[i].getEnd() == sequence.findPosition(res)) - { - if (tooltipText.length() > 6) - tooltipText.append("
"); - tooltipText.append("disulfide bond " + features[i].getBegin() + ":" + - features[i].getEnd()); - if (features[i].links != null) - tooltipText.append(" "); - } - } - else - { - if (tooltipText.length() > 6) - tooltipText.append("
"); - - tooltipText.append(features[i].getType() + " " + - features[i].begin); - if (features[i].begin != features[i].end) - tooltipText.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) - { - tooltipText.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(">", ">"); - - tooltipText.append("; "); - tooltipText.append(tmpString); - - } - else - tooltipText.append("; "+tmpString); - } - } - if (features[i].getValue("status") != null ) - { - String status = features[i].getValue("status").toString(); - if(status.length()>0) - tooltipText.append("; (" + features[i].getValue("status") + ")"); - } - - if (features[i].links != null) - tooltipText.append(" "); - - } - - // else if(features[i].begin==0 && features[i].end==0) - { - // seqSpecific.append(features[i].featureGroup+": " - // + features[i].getType()+" " - // +features[i].getDescription()+"
"); - - } + 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(tooltipText.length()==6) // + if (startTag > -1) { - setToolTipText(null); + tooltipText.append("; " + tmpString); } else { - tooltipText.append(""); - setToolTipText(tooltipText.toString()); - } - } - else - setToolTipText(null); - } - } + 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(">", ">"); - void setStatusMessage(SequenceI sequence, int res, int seq) - { - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); + tooltipText.append("; "); + tooltipText.append(tmpString); - Object obj = null; - if (av.alignment.isNucleotide()) - { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + - ""); - if (obj != null) - text.append(" Nucleotide: "); - } - else - { - obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); - if (obj != null) - text.append(" Residue: "); - } + } + else + { + tooltipText.append("; " + tmpString); + } + } + } + if (features[i].getValue("status") != null) + { + String status = features[i].getValue("status").toString(); + if (status.length() > 0) + { + tooltipText.append("; (" + features[i].getValue("status") + ")"); + } + } - if (obj != null) - { + if (features[i].links != null) + { + tooltipText.append(" "); + } - if (obj != "") - { - text.append(obj + " (" + sequence.findPosition(res) + - ")"); + } } } - ap.alignFrame.statusBar.setText(text.toString()); + } + + if (tooltipText.length() == 6) // + { + setToolTipText(null); + } + else + { + tooltipText.append(""); + setToolTipText(tooltipText.toString()); + } + // else + // setToolTipText(null); + } + + void setStatusMessage(SequenceI sequence, int res, int seq) + { + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); + Object obj = null; + if (av.alignment.isNucleotide()) + { + obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + + ""); + if (obj != null) + { + text.append(" Nucleotide: "); + } + } + else + { + obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + if (obj != null) + { + text.append(" Residue: "); + } } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseDragged(MouseEvent evt) + if (obj != null) { - if (mouseWheelPressed) + + if (obj != "") { - int oldWidth = av.charWidth; + text.append(obj + " (" + sequence.findPosition(res) + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); - //Which is bigger, left-right or up-down? - if (Math.abs(evt.getY() - lastMousePress.getY()) - > Math.abs(evt.getX() - lastMousePress.getX())) - { - int fontSize = av.font.getSize(); + } - if (evt.getY() < lastMousePress.getY()) - { - fontSize--; - } - else if (evt.getY() > lastMousePress.getY()) - { - fontSize++; - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseDragged(MouseEvent evt) + { + if (mouseWheelPressed) + { + int oldWidth = av.charWidth; - if(fontSize<1) - fontSize = 1; + //Which is bigger, left-right or up-down? + if (Math.abs(evt.getY() - lastMousePress.getY()) + > Math.abs(evt.getX() - lastMousePress.getX())) + { + int fontSize = av.font.getSize(); - av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); - av.charWidth = oldWidth; - ap.fontChanged(); + if (evt.getY() < lastMousePress.getY()) + { + fontSize--; } - else + else if (evt.getY() > lastMousePress.getY()) { - if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) - { - av.charWidth--; - } - else if (evt.getX() > lastMousePress.getX()) - { - av.charWidth++; - } + fontSize++; + } + + if (fontSize < 1) + { + fontSize = 1; + } - ap.repaint(); + av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); + av.charWidth = oldWidth; + ap.fontChanged(); + } + else + { + if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) + { + av.charWidth--; } + else if (evt.getX() > lastMousePress.getX()) + { + av.charWidth++; + } + + ap.repaint(); + } - FontMetrics fm = getFontMetrics(av.getFont()); - av.validCharWidth = fm.charWidth('M') <= av.charWidth; + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.charWidth; - lastMousePress = evt.getPoint(); + lastMousePress = evt.getPoint(); - return; + return; + } + + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } + + int res = findRes(evt); + + if (res < 0) + { + res = 0; + } + + if ( (lastres == -1) || (lastres == res)) + { + return; + } + + if ( (res < av.getAlignment().getWidth()) && (res < lastres)) + { + // dragLeft, delete gap + editSequence(false, res); + } + else + { + editSequence(true, res); + } + + mouseDragging = true; + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } + + } + + synchronized void editSequence(boolean insertGap, int startres) + { + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); + + SequenceI seq = av.alignment.getSequenceAt(startseq); + + //No group, but the sequence may represent a group + if (!groupEditing && av.hasHiddenRows) + { + if (av.hiddenRepSequences != null + && av.hiddenRepSequences.containsKey(seq)) + { + sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + groupEditing = true; } + } - if (!editingSeqs) + StringBuffer message = new StringBuffer(); + if (groupEditing) + { + message.append("Edit group:"); + if (editCommand == null) { - doMouseDraggedDefineMode(evt); - return; + editCommand = new EditCommand("Edit Group"); } + } + else + { + message.append("Edit sequence: " + seq.getName()); + String label = seq.getName(); + if (label.length() > 10) + { + label = label.substring(0, 10); + } + if (editCommand == null) + { + editCommand = new EditCommand("Edit " + label); + } + } + + if (insertGap) + { + message.append(" insert "); + } + else + { + message.append(" delete "); + } - int res = findRes(evt); + message.append(Math.abs(startres - lastres) + " gaps."); + ap.alignFrame.statusBar.setText(message.toString()); - if (res < 0) - { - res = 0; - } + //Are we editing within a selection group? + if (groupEditing + || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq))) + { + fixedColumns = true; - if ((lastres == -1) || (lastres == res)) + //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)) { - return; + endEditing(); + return; } + sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + } - if ( (res < av.getAlignment().getWidth()) && (res < lastres)) - { - // dragLeft, delete gap - editSequence(false, res); - } - else - editSequence(true, res); + fixedLeft = sg.getStartRes(); + fixedRight = sg.getEndRes(); - mouseDragging = true; - if(scrollThread!=null) - scrollThread.setEvent(evt); + if ( (startres < fixedLeft && lastres >= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <= fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) + { + endEditing(); + return; + } + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } } - synchronized void editSequence(boolean insertGap, int startres) + if (av.hasHiddenColumns) { - int fixedLeft = -1; - int fixedRight = -1; - boolean fixedColumns = false; - SequenceGroup sg = av.getSelectionGroup(); - - SequenceI seq = av.alignment.getSequenceAt(startseq); - - //No group, but the sequence may represent a group - if (!groupEditing && av.hasHiddenRows) - { - if (av.hiddenRepSequences!=null - && av.hiddenRepSequences.containsKey(seq)) - { - sg = (SequenceGroup)av.hiddenRepSequences.get(seq); - groupEditing = true; - } - } + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + if ( (insertGap && startres > y1 && lastres < y1) + || (!insertGap && startres < y2 && lastres > y2)) + { + endEditing(); + return; + } - StringBuffer message = new StringBuffer(); - if (groupEditing) + //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + //Selection spans a hidden region + if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) + { + if (startres >= y2) { - message.append("Edit group:"); - if (editCommand == null) - editCommand = new EditCommand("Edit Group"); + fixedLeft = y2; } else - { - message.append("Edit sequence: " + seq.getName()); - String label = seq.getName(); - if(label.length()>10) - label = label.substring(0,10); - if(editCommand==null) - editCommand = new EditCommand("Edit "+label); - } - - if(insertGap) - message.append(" insert "); - else - message.append(" delete "); - - message.append(Math.abs(startres-lastres)+" gaps."); - ap.alignFrame.statusBar.setText(message.toString()); - - - //Are we editing within a selection group? - if (groupEditing - || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq))) { - fixedColumns = true; + fixedRight = y2 - 1; + } + } + } - //sg might be null as the user may only see 1 sequence, - //but the sequence represents a group - if (sg == null) - { - sg = (SequenceGroup) av.hiddenRepSequences.get(seq); - } + 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); + } - fixedLeft = sg.getStartRes(); + // drag to right + if (insertGap) + { + //If the user has selected the whole sequence, and is dragging to + // the right, we can still extend the alignment and selectionGroup + if (sg.getStartRes() == 0 + && sg.getEndRes() == fixedRight + && sg.getEndRes() == av.alignment.getWidth() - 1 + ) + { + sg.setEndRes(av.alignment.getWidth() + startres - lastres); fixedRight = sg.getEndRes(); + } - if ( (startres < fixedLeft && lastres >= fixedLeft) - || (startres >= fixedLeft && lastres < fixedLeft) - || (startres > fixedRight && lastres <=fixedRight) - || (startres <= fixedRight && lastres > fixedRight)) - { - endEditing(); - return; - } + // Is it valid with fixed columns?? + // Find the next gap before the end + // of the visible region boundary + boolean blank = false; + for (fixedRight = fixedRight; + fixedRight > lastres; + fixedRight--) + { + blank = true; - if (fixedLeft > startres) + for (g = 0; g < groupSize; g++) { - fixedRight = fixedLeft - 1; - fixedLeft = 0; + for (int j = 0; j < startres - lastres; j++) + { + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(fixedRight - j))) + { + blank = false; + break; + } + } } - else if (fixedRight < startres) + if (blank) { - fixedLeft = fixedRight; - fixedRight = -1; + break; } } - - if(av.hasHiddenColumns ) + if (!blank) { - 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 (sg.getSize() == av.alignment.getHeight()) + { + if ( (av.hasHiddenColumns + && + startres < av.getColumnSelection().getHiddenBoundaryRight(startres))) { endEditing(); return; } - //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); - //Selection spans a hidden region - if(fixedLefty2 || fixedRight==-1)) + int alWidth = av.alignment.getWidth(); + if (av.hasHiddenRows) { - if(startres>=y2) + int hwidth = av.alignment.getHiddenSequences().getWidth(); + if (hwidth > alWidth) { - fixedLeft = y2; + alWidth = hwidth; } - else - { - fixedRight = y2 - 1; - } } + //We can still insert gaps if the selectionGroup + //contains all the sequences + sg.setEndRes(sg.getEndRes() + startres - lastres); + fixedRight = alWidth + startres - lastres; + } + else + { + endEditing(); + return; + } } + } + // drag to left + else if (!insertGap) + { + /// Are we able to delete? + // ie are all columns blank? - if (groupEditing) + for (g = 0; g < groupSize; g++) { - Vector vseqs = sg.getSequences(av.hiddenRepSequences); - int g, groupSize = vseqs.size(); - SequenceI[] groupSeqs = new SequenceI[groupSize]; - for (g = 0; g < groupSeqs.length; g++) - groupSeqs[g] = (SequenceI) vseqs.elementAt(g); - - // drag to right - if (insertGap) + for (int j = startres; j < lastres; j++) { - //If the user has selected the whole sequence, and is dragging to - // the right, we can still extend the alignment and selectionGroup - if( sg.getStartRes() == 0 - && sg.getEndRes() == fixedRight - && sg.getEndRes() == av.alignment.getWidth()-1 - ) - { - sg.setEndRes(av.alignment.getWidth() + startres - lastres); - fixedRight = sg.getEndRes(); - } - - // Is it valid with fixed columns?? - // Find the next gap before the end - // of the visible region boundary - boolean blank = false; - for (fixedRight = fixedRight; - fixedRight > lastres; - fixedRight--) + if (groupSeqs[g].getLength() <= j) { - blank = true; - - for (g = 0; g < groupSize; g++) - { - for (int j = 0; j < startres - lastres; j++) - { - if (!jalview.util.Comparison.isGap( - groupSeqs[g].getCharAt(fixedRight - j))) - { - blank = false; - break; - } - } - } - if (blank) - break; + continue; } - if (!blank) + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(j))) { - if(sg.getSize() == av.alignment.getHeight() ) - { - if((av.hasHiddenColumns - && startresalWidth) - alWidth = hwidth; - } - //We can still insert gaps if the selectionGroup - //contains all the sequences - sg.setEndRes(sg.getEndRes()+startres-lastres); - fixedRight = alWidth+startres-lastres; - } - else - { - endEditing(); - return; - } + // Not a gap, block edit not valid + endEditing(); + return; } } + } + } - - // drag to left - else if(!insertGap) + if (insertGap) + { + // dragging to the right + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) { - /// Are we able to delete? - // ie are all columns blank? - - for (g = 0; g < groupSize; g++) - { - for (int j = startres; j < lastres; j++) - { - if (groupSeqs[g].getLength() <= j) - { - continue; - } - - if (!jalview.util.Comparison.isGap( - groupSeqs[g].getCharAt(j))) - { - // Not a gap, block edit not valid - endEditing(); - return; - } - } - } + insertChar(j, groupSeqs, fixedRight); } + } + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + groupSeqs, + startres, startres - lastres, + av.alignment, + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j > startres; j--) + { + deleteChar(startres, groupSeqs, fixedRight); + } + } + else + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + groupSeqs, + startres, lastres - startres, + av.alignment, + true); + } - if (insertGap) - { - // dragging to the right - if (fixedColumns && fixedRight != -1) - { - for (int j = lastres; j < startres; j++) - { - insertChar(j, groupSeqs, fixedRight); - } - } - else - { - editCommand.appendEdit(EditCommand.INSERT_GAP, - groupSeqs, - startres, startres-lastres, - av.alignment, - true); - } - } - else - { - // dragging to the left - if (fixedColumns && fixedRight != -1) - { - for (int j = lastres; j > startres; j--) - { - deleteChar(startres, groupSeqs, fixedRight); - } - } - else - editCommand.appendEdit(EditCommand.DELETE_GAP, - groupSeqs, - startres, lastres - startres, - av.alignment, - true); - - } + } + } + else /////Editing a single sequence/////////// + { + if (insertGap) + { + // dragging to the right + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, new SequenceI[] + {seq}, fixedRight); + } } - else /////Editing a single sequence/////////// + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + new SequenceI[] + {seq}, + lastres, startres - lastres, + av.alignment, + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) { - if (insertGap) + for (int j = lastres; j > startres; j--) { - // dragging to the right - if (fixedColumns && fixedRight != -1) + if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) { - for (int j = lastres; j < startres; j++) - { - insertChar(j, new SequenceI[]{seq}, fixedRight); - } - } - else - { - editCommand.appendEdit(EditCommand.INSERT_GAP, - new SequenceI[] - {seq}, - lastres, startres-lastres, - av.alignment, - true); + endEditing(); + break; } + deleteChar(startres, new SequenceI[] + {seq}, fixedRight); } - else + } + else + { + //could be a keyboard edit trying to delete none gaps + int max = 0; + for (int m = startres; m < lastres; m++) { - // dragging to the left - if (fixedColumns && fixedRight != -1) + if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) { - for (int j = lastres; j > startres; j--) - { - if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) - { - endEditing(); - break; - } - deleteChar(startres, new SequenceI[]{seq}, fixedRight); - } + break; } - else - { - //could be a keyboard edit trying to delete none gaps - int max=0; - for(int m = startres; m0) - { - editCommand.appendEdit(EditCommand.DELETE_GAP, - new SequenceI[] - {seq}, - startres, max, - av.alignment, - true); - } - } + if (max > 0) + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + new SequenceI[] + {seq}, + startres, max, + av.alignment, + true); } } + } + } + + lastres = startres; + seqCanvas.repaint(); + } + + void insertChar(int j, SequenceI[] seq, int fixedColumn) + { + int blankColumn = fixedColumn; + for (int s = 0; s < seq.length; s++) + { + //Find the next gap before the end of the visible region boundary + //If lastCol > j, theres a boundary after the gap insertion + + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) + { + if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } + } - lastres = startres; - seqCanvas.repaint(); + if (blankColumn <= j) + { + blankColumn = fixedColumn; + endEditing(); + return; + } } + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + blankColumn, 1, av.alignment, true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + j, 1, av.alignment, + true); + + } + + void deleteChar(int j, SequenceI[] seq, int fixedColumn) + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + j, 1, av.alignment, true); - void insertChar(int j, SequenceI [] seq, int fixedColumn) + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + fixedColumn, 1, av.alignment, true); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) + { + if (oldSeq < 0) + { + oldSeq = 0; + } + + if (scrollThread != null) { - int blankColumn = fixedColumn; - for(int s=0; s 1) + { + if (av.getSelectionGroup().getSize() == 1 + && av.getSelectionGroup().getEndRes() + - av.getSelectionGroup().getStartRes() < 2) { - //Find the next gap before the end of the visible region boundary - //If lastCol > j, theres a boundary after the gap insertion + av.setSelectionGroup(null); + } - for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) - { - if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) - { - //Theres a space, so break and insert the gap - break; - } - } + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + sequence.findPosition(findRes(evt)) + ); - if (blankColumn <= j) - { - blankColumn = fixedColumn; - endEditing(); - return; - } + if (features != null && features.length > 0) + { + SearchResults highlight = new SearchResults(); + highlight.addResult(sequence, + features[0].getBegin(), + features[0].getEnd()); + seqCanvas.highlightSearchResults(highlight); } + if (features != null && features.length > 0) + { + seqCanvas.getFeatureRenderer().amendFeatures( + new SequenceI[] + {sequence}, features, false, ap); + + seqCanvas.highlightSearchResults(null); + } + } + } + + public void mouseWheelMoved(MouseWheelEvent e) + { + e.consume(); + /* if (mouseWheelPressed) + { + Font font = av.getFont(); + int fontSize = font.getSize(); + if (e.getWheelRotation() > 0 && fontSize < 51) + fontSize++; + else if (fontSize > 1) + fontSize--; + + + + av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); + + ap.fontChanged(); + } + else*/ + { + if (e.getWheelRotation() > 0) + { + ap.scrollUp(false); + } + else + { + ap.scrollUp(true); + } + } + + } - editCommand.appendEdit(EditCommand.DELETE_GAP, - seq, - blankColumn, 1, av.alignment, true); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMousePressedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int seq = findSeq(evt); + oldSeq = seq; - editCommand.appendEdit(EditCommand.INSERT_GAP, - seq, - j, 1, av.alignment, - true); + startWrapBlock = wrappedBlock; + if (av.wrapAlignment && seq > av.alignment.getHeight()) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Cannot edit annotations in wrapped view.", + "Wrapped view - no edit", + JOptionPane.WARNING_MESSAGE); + return; } - void deleteChar(int j, SequenceI [] seq, int fixedColumn) + if (seq < 0 || res < 0) { + return; + } - editCommand.appendEdit(EditCommand.DELETE_GAP, - seq, - j, 1, av.alignment, true); + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); - editCommand.appendEdit(EditCommand.INSERT_GAP, - seq, - fixedColumn, 1, av.alignment, true); + if ( (sequence == null) || (res > sequence.getLength())) + { + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseEntered(MouseEvent e) + stretchGroup = av.getSelectionGroup(); + + if (stretchGroup == null) { - if(oldSeq < 0) - oldSeq = 0; + stretchGroup = av.alignment.findGroup(sequence); - if (scrollThread != null) - { - scrollThread.running = false; - scrollThread = null; - } + if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) && + (res < stretchGroup.getEndRes())) + { + av.setSelectionGroup(stretchGroup); + } + else + { + stretchGroup = null; + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseExited(MouseEvent e) + else if (!stretchGroup.getSequences(null).contains(sequence) || + (stretchGroup.getStartRes() > res) || + (stretchGroup.getEndRes() < res)) { - if (av.getWrapAlignment()) - { - return; - } + stretchGroup = null; - if (mouseDragging) + SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + + if (allGroups != null) + { + for (int i = 0; i < allGroups.length; i++) { - scrollThread = new ScrollThread(); + if ( (allGroups[i].getStartRes() <= res) && + (allGroups[i].getEndRes() >= res)) + { + stretchGroup = allGroups[i]; + break; + } } + } + + av.setSelectionGroup(stretchGroup); + } - public void mouseClicked(MouseEvent evt) + if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) ); - if(evt.getClickCount()>1) + Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + Vector links = new Vector(); + for (int i = 0; i < allFeatures.size(); i++) { - if (av.getSelectionGroup().getSize() == 1 - && av.getSelectionGroup().getEndRes() - - av.getSelectionGroup().getStartRes() < 2) - av.setSelectionGroup(null); - - SequenceFeature[] features = findFeaturesAtRes( - sequence.getDatasetSequence(), - sequence.findPosition( findRes(evt) ) - ); - - if(features!=null && features.length>0) - { - SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, - features[0].getBegin(), - features[0].getEnd()); - seqCanvas.highlightSearchResults(highlight); - } - if(features!=null && features.length>0) + SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); + if (sf.links != null) { - seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] - {sequence}, features, false, ap); - - seqCanvas.highlightSearchResults(null); + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); + } } } + + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); + pop.show(this, evt.getX(), evt.getY()); + return; } - public void mouseWheelMoved(MouseWheelEvent e) + if (av.cursorMode) { - e.consume(); - /* if (mouseWheelPressed) - { - Font font = av.getFont(); - int fontSize = font.getSize(); - if (e.getWheelRotation() > 0 && fontSize < 51) - fontSize++; - else if (fontSize > 1) - fontSize--; + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } + if (stretchGroup == null) + { + //Only if left mouse button do we want to change group sizes + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; - av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), + "Background"); + } - ap.fontChanged(); + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); } - else*/ + if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res)) { - if (e.getWheelRotation() > 0) - ap.scrollUp(false); - else - ap.scrollUp(true); + // Edit end res position of selected group + changeEndRes = true; } - + else if ( (stretchGroup != null) && + (stretchGroup.getStartRes() == res)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); } + seqCanvas.repaint(); + } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMousePressedDefineMode(MouseEvent evt) + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseReleasedDefineMode(MouseEvent evt) + { + if (stretchGroup == null) { - int res = findRes(evt); - int seq = findSeq(evt); - oldSeq = seq; - - startWrapBlock=wrappedBlock; + return; + } - if(av.wrapAlignment && seq>av.alignment.getHeight()) + if (stretchGroup.cs != null) + { + if (stretchGroup.cs instanceof ClustalxColourScheme) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Cannot edit annotations in wrapped view.", - "Wrapped view - no edit", - JOptionPane.WARNING_MESSAGE); - return; + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(av.hiddenRepSequences), + stretchGroup.getWidth()); } - if(seq<0 || res<0) - return; - - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); - - if ((sequence == null) || (res > sequence.getLength())) - { - return; - } - - stretchGroup = av.getSelectionGroup(); - - if (stretchGroup == null) - { - stretchGroup = av.alignment.findGroup(sequence); - - if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && - (res < stretchGroup.getEndRes())) - { - av.setSelectionGroup(stretchGroup); - } - else - { - stretchGroup = null; - } - } - else if (!stretchGroup.getSequences(null).contains(sequence) || - (stretchGroup.getStartRes() > res) || - (stretchGroup.getEndRes() < res)) - { - stretchGroup = null; - - SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); - - if (allGroups != null) - { - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) && - (allGroups[i].getEndRes() >= res)) - { - stretchGroup = allGroups[i]; - break; - } - } - } - - av.setSelectionGroup(stretchGroup); - - } - - - if (javax.swing.SwingUtilities.isRightMouseButton(evt)) - { - Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); - Vector links = new Vector(); - for (int i = 0; i < allFeatures.size(); i++) - { - SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); - if (sf.links != null) - { - for (int j = 0; j < sf.links.size(); j++) - { - links.addElement(sf.links.elementAt(j)); - } - } - } - - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); - pop.show(this, evt.getX(), evt.getY()); - return; - } - - if (av.cursorMode) - { - seqCanvas.cursorX = findRes(evt); - seqCanvas.cursorY = findSeq(evt); - seqCanvas.repaint(); - return; - } - - if (stretchGroup == null) - { - //Only if left mouse button do we want to change group sizes + if (stretchGroup.cs instanceof Blosum62ColourScheme + || stretchGroup.cs instanceof PIDColourScheme + || stretchGroup.cs.conservationApplied() + || stretchGroup.cs.getThreshold() > 0) + { + stretchGroup.recalcConservation(); + } - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; + if (stretchGroup.cs.conservationApplied()) + { + SliderPanel.setConservationSlider(ap, stretchGroup.cs, + stretchGroup.getName()); + } + else + { + SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, + stretchGroup.getName()); + } + } + changeEndRes = false; + changeStartRes = false; + stretchGroup = null; - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, - av.getGlobalColourScheme(), - "Background"); - } + PaintRefresher.Refresh(this, av.getSequenceSetId()); + } - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); - } - if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { - // Edit end res position of selected group - changeEndRes = true; - } - else if ( (stretchGroup != null) && - (stretchGroup.getStartRes() == res)) - { - // Edit end res position of selected group - changeStartRes = true; - } - stretchGroup.getWidth(); - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseDraggedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int y = findSeq(evt); - seqCanvas.repaint(); + if (wrappedBlock != startWrapBlock) + { + return; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseReleasedDefineMode(MouseEvent evt) + if (stretchGroup == null) { - if (stretchGroup == null) - { - return; - } - - - if(stretchGroup.cs!=null) - { - if (stretchGroup.cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( - stretchGroup.getSequences(av.hiddenRepSequences), - stretchGroup.getWidth()); - } - - if (stretchGroup.cs instanceof Blosum62ColourScheme - || stretchGroup.cs instanceof PIDColourScheme - || stretchGroup.cs.conservationApplied() - || stretchGroup.cs.getThreshold()>0) - stretchGroup.recalcConservation(); + return; + } - if (stretchGroup.cs.conservationApplied()) - { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, - stretchGroup.getName()); - } - else - { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); - } - } - changeEndRes = false; - changeStartRes = false; - stretchGroup = null; + if (res >= av.alignment.getWidth()) + { + res = av.alignment.getWidth() - 1; + } - PaintRefresher.Refresh(this, av.getSequenceSetId()); + if (stretchGroup.getEndRes() == res) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if (stretchGroup.getStartRes() == res) + { + // Edit start res position of selected group + changeStartRes = true; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseDraggedDefineMode(MouseEvent evt) + if (res < av.getStartRes()) { - int res = findRes(evt); - int y = findSeq(evt); + res = av.getStartRes(); + } - if(wrappedBlock!=startWrapBlock) - return; + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) + { + stretchGroup.setEndRes(res); + } + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) + { + stretchGroup.setStartRes(res); + } + } - if (stretchGroup == null) - { - return; - } + int dragDirection = 0; - if(res>= av.alignment.getWidth()) - { - res = av.alignment.getWidth()-1; - } + if (y > oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } - if (stretchGroup.getEndRes() == res) - { - // Edit end res position of selected group - changeEndRes = true; - } - else if (stretchGroup.getStartRes() == res) - { - // Edit start res position of selected group - changeStartRes = true; - } + while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + { + // This routine ensures we don't skip any sequences, as the + // selection is quite slow. + Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - if (res < av.getStartRes()) - { - res = av.getStartRes(); - } + oldSeq += dragDirection; - if (changeEndRes) - { - if (res > (stretchGroup.getStartRes() - 1)) - { - stretchGroup.setEndRes(res); - } - } - else if (changeStartRes) - { - if (res < (stretchGroup.getEndRes() + 1)) - { - stretchGroup.setStartRes(res); - } - } + if (oldSeq < 0) + { + break; + } - int dragDirection = 0; + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - if (y > oldSeq) - { - dragDirection = 1; - } - else if (y < oldSeq) + if (stretchGroup.getSequences(null).contains(nextSeq)) + { + stretchGroup.deleteSequence(seq, false); + } + else + { + if (seq != null) { - dragDirection = -1; + stretchGroup.addSequence(seq, false); } + stretchGroup.addSequence(nextSeq, false); + } + } - while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) - { - // This routine ensures we don't skip any sequences, as the - // selection is quite slow. - Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - - oldSeq += dragDirection; + if (oldSeq < 0) + { + oldSeq = -1; + } - if(oldSeq<0) - break; + mouseDragging = true; - Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } - if (stretchGroup.getSequences(null).contains(nextSeq)) - { - stretchGroup.deleteSequence(seq, false); - } - else - { - if (seq != null) - { - stretchGroup.addSequence(seq, false); - } + seqCanvas.repaint(); + } - stretchGroup.addSequence(nextSeq, false); - } - } + void scrollCanvas(MouseEvent evt) + { + if (evt == null) + { + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } + mouseDragging = false; + } + else + { + if (scrollThread == null) + { + scrollThread = new ScrollThread(); + } - if(oldSeq < 0) - oldSeq = -1; + mouseDragging = true; + scrollThread.setEvent(evt); + } - mouseDragging = true; + } - if (scrollThread != null) - { - scrollThread.setEvent(evt); - } + // this class allows scrolling off the bottom of the visible alignment + class ScrollThread + extends Thread + { + MouseEvent evt; + boolean running = false; - seqCanvas.repaint(); + public ScrollThread() + { + start(); } - void scrollCanvas(MouseEvent evt) + public void setEvent(MouseEvent e) { - if(evt==null) - { - if(scrollThread!=null) - { - scrollThread.running = false; - scrollThread = null; - } - mouseDragging = false; - } - else - { - if (scrollThread == null) - scrollThread = new ScrollThread(); - - mouseDragging = true; - scrollThread.setEvent(evt); - } - + evt = e; } + public void stopScrolling() + { + running = false; + } - // this class allows scrolling off the bottom of the visible alignment - class ScrollThread extends Thread + public void run() { - MouseEvent evt; - boolean running = false; + running = true; - public ScrollThread() + while (running) + { + if (evt != null) { - start(); - } + if (mouseDragging && (evt.getY() < 0) && + (av.getStartSeq() > 0)) + { + running = ap.scrollUp(true); + } - public void setEvent(MouseEvent e) - { - evt = e; + if (mouseDragging && (evt.getY() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) + { + running = ap.scrollUp(false); + } + + if (mouseDragging && (evt.getX() < 0)) + { + running = ap.scrollRight(false); + } + else if (mouseDragging && (evt.getX() >= getWidth())) + { + running = ap.scrollRight(true); + } } - public void stopScrolling() + try { - running = false; + Thread.sleep(20); } - - public void run() + catch (Exception ex) { - running = true; - - while (running) - { - if (evt != null) - { - if (mouseDragging && (evt.getY() < 0) && - (av.getStartSeq() > 0)) - { - running = ap.scrollUp(true); - } - - if (mouseDragging && (evt.getY() >= getHeight()) && - (av.alignment.getHeight() > av.getEndSeq())) - { - running = ap.scrollUp(false); - } - - if (mouseDragging && (evt.getX() < 0)) - { - running = ap.scrollRight(false); - } - else if (mouseDragging && (evt.getX() >= getWidth())) - { - running = ap.scrollRight(true); - } - } - - try - { - Thread.sleep(20); - } - catch (Exception ex) - { - } - } } + } } + } }