X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=d45759343751073e7574c9aca7e9939bf29b81ee;hb=94e3d91558ad96de545821aeb548934f8c8353a3;hp=8486ac1f59f78c5ef76080d5a16f2d3367a36ed6;hpb=ce728f87f1f43be3041ef02f7f2cc2e39314711a;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 8486ac1..d457593 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -18,8 +18,6 @@ */ package jalview.gui; -import jalview.analysis.*; - import jalview.datamodel.*; import jalview.schemes.*; @@ -27,10 +25,10 @@ import jalview.schemes.*; import java.awt.*; import java.awt.event.*; -import java.util.*; - import javax.swing.*; +import java.util.Vector; + /** * DOCUMENT ME! @@ -38,7 +36,9 @@ import javax.swing.*; * @author $author$ * @version $Revision$ */ -public class SeqPanel extends JPanel +public class SeqPanel extends JPanel implements MouseListener, + MouseMotionListener, MouseWheelListener + { /** DOCUMENT ME!! */ public SeqCanvas seqCanvas; @@ -47,12 +47,10 @@ public class SeqPanel extends JPanel public AlignmentPanel ap; protected int lastres; protected int startseq; - int startEdit = -1; - int endEdit = -1; protected AlignViewport av; // if character is inserted or deleted, we will need to recalculate the conservation - int seqEditOccurred = -1; + boolean seqEditOccurred = false; ScrollThread scrollThread = null; boolean mouseDragging = false; boolean editingSeqs = false; @@ -69,7 +67,12 @@ public class SeqPanel extends JPanel SequenceGroup stretchGroup = null; boolean remove = false; + Point lastMousePress; boolean mouseWheelPressed = false; + StringBuffer keyboardNo1; + StringBuffer keyboardNo2; + + java.net.URL linkImageURL; /** * Creates a new SeqPanel object. @@ -79,6 +82,7 @@ public class SeqPanel extends JPanel */ public SeqPanel(AlignViewport avp, AlignmentPanel p) { + linkImageURL = getClass().getResource("/images/link.gif"); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -91,116 +95,12 @@ public class SeqPanel extends JPanel ap = p; - addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { - doMouseMoved(evt); - } - - public void mouseDragged(MouseEvent evt) - { - if (editingSeqs) - { - doMouseDragged(evt); - } - else - { - doMouseDraggedDefineMode(evt); - } - } - }); - - addMouseWheelListener(new MouseWheelListener() - { - public void mouseWheelMoved(MouseWheelEvent e) - { - - if (mouseWheelPressed) - { - Font font = av.getFont(); - int fontSize = font.getSize(); - if (e.getWheelRotation() > 0 && fontSize < 30) - 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); - } - - } - }); - - - addMouseListener(new MouseAdapter() - { - public void mouseReleased(MouseEvent evt) - { - mouseWheelPressed = false; - - if (editingSeqs) - { - doMouseReleased(evt); - } - else - { - doMouseReleasedDefineMode(evt); - } - } - - public void mousePressed(MouseEvent evt) - { - if( javax.swing.SwingUtilities.isMiddleMouseButton(evt)) - { - mouseWheelPressed = true; - return; - } - - if (evt.isShiftDown() || evt.isAltDown() || - evt.isControlDown()) - { - if (evt.isAltDown() || evt.isControlDown()) - { - groupEditing = true; - } - - editingSeqs = true; - doMousePressed(evt); - } - else - { - doMousePressedDefineMode(evt); - } - } - - public void mouseExited(MouseEvent evt) - { - if (editingSeqs) - { - return; - } - - doMouseExitedDefineMode(evt); - } - - public void mouseEntered(MouseEvent evt) - { - if (editingSeqs) - { - return; - } - - doMouseEnteredDefineMode(evt); - } - }); + if(!av.isDataset()) + { + addMouseMotionListener(this); + addMouseListener(this); + addMouseWheelListener(this); + } } int startWrapBlock=-1; @@ -238,6 +138,9 @@ public class SeqPanel extends JPanel res = (x / av.getCharWidth()) + av.getStartRes(); } + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + return res; } @@ -269,37 +172,296 @@ public class SeqPanel extends JPanel return seq; } + Vector getAllFeaturesAtRes(SequenceI seq, int res) + { + Vector allFeatures = new Vector(); + int index = 0; + if(seq.getSequenceFeatures()!=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() + { + startseq = -1; + lastres = -1; + seqEditOccurred = false; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + } + + void setCursorRow() + { + seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorRowAndColumn() + { + if(keyboardNo2==null) + { + keyboardNo2 = new StringBuffer(); + } + else + { + 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 moveCursor(int dx, int dy) + { + seqCanvas.cursorX += dx; + seqCanvas.cursorY += dy; + scrollToVisible(); + } + + void scrollToVisible() + { + if (seqCanvas.cursorX < 0) + seqCanvas.cursorX = 0; + else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) + seqCanvas.cursorX = av.alignment.getWidth() - 1; + + if (seqCanvas.cursorY < 0) + seqCanvas.cursorY = 0; + else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + seqCanvas.cursorY = av.alignment.getHeight() - 1; + + + endEditing(); + if(av.wrapAlignment) + { + ap.scrollToWrappedVisible(seqCanvas.cursorX); + } + else + { + while (seqCanvas.cursorY < av.startSeq) + { + ap.scrollUp(true); + } + while (seqCanvas.cursorY + 1 > av.endSeq) + { + ap.scrollUp(false); + } + if (!av.wrapAlignment) + { + while (seqCanvas.cursorX < av.startRes) + { + if (!ap.scrollRight(false)) + break; + } + while (seqCanvas.cursorX > av.endRes) + { + if (!ap.scrollRight(true)) + break; + } + } + } + setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + seqCanvas.cursorX, seqCanvas.cursorY); + + seqCanvas.repaint(); + } + + void setSelectionAreaAtCursor(boolean topLeft) + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + + if(av.getSelectionGroup()!=null) + { + SequenceGroup sg = av.selectionGroup; + //Find the top and bottom of this group + int min = av.alignment.getHeight(), max = 0; + for(int i=0; i max) + max = index; + if(index < min) + min = index; + } + + max ++; + + if(topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if(sg.getEndRes()seqCanvas.cursorX) + sg.setStartRes(seqCanvas.cursorX); + + max = seqCanvas.cursorY+1; + } + + if(min>max) + { + // Only the user can do this + av.setSelectionGroup(null); + } + else + { + // Now add any sequences between min and max + sg.sequences.clear(); + for (int i = min; i < max; i++) + { + sg.addSequence(av.alignment.getSequenceAt(i), false); + } + } + } + + if (av.getSelectionGroup() == null) + { + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(seqCanvas.cursorX); + sg.setEndRes(seqCanvas.cursorX); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + } + + + ap.repaint(); + } + + void insertGapAtCursor(boolean group) + { + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); + editOccurred(); + } + + void deleteGapAtCursor(boolean group) + { + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); + editSequence(false, seqCanvas.cursorX); + editOccurred(); + } + + void numberPressed(char value) + { + if(keyboardNo1==null) + keyboardNo1 = new StringBuffer(); + + if(keyboardNo2!=null) + keyboardNo2.append(value); + else + keyboardNo1.append(value); + } + + int getKeyboardNo(StringBuffer kb) + { + if(kb==null) + return 1; + else + return Integer.parseInt(kb.toString()); + } + /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ - public void doMouseReleased(MouseEvent evt) + public void mouseReleased(MouseEvent evt) { - if (seqEditOccurred > -1) - { - editOccurred(seqEditOccurred); - } + mouseDragging = false; + mouseWheelPressed = false; - startseq = -1; - lastres = -1; - seqEditOccurred = -1; - editingSeqs = false; - groupEditing = false; + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } + + editOccurred(); - ap.repaint(); + endEditing(); + ap.repaint(); } + + /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ - public void doMousePressed(MouseEvent evt) + public void mousePressed(MouseEvent evt) { - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); + lastMousePress = evt.getPoint(); + + if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + { + mouseWheelPressed = true; + 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); @@ -307,6 +469,9 @@ public class SeqPanel extends JPanel if(seq<0 || res<0) return; + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); + if ((seq < av.getAlignment().getHeight()) && (res < av.getAlignment().getSequenceAt(seq).getLength())) { @@ -319,9 +484,6 @@ public class SeqPanel extends JPanel lastres = -1; } - startEdit = lastres; - endEdit = lastres; - return; } @@ -330,11 +492,19 @@ public class SeqPanel extends JPanel * * @param evt DOCUMENT ME! */ - public void doMouseMoved(MouseEvent evt) + public void mouseMoved(MouseEvent evt) { + if (editingSeqs) + { + // This is because MacOSX creates a mouseMoved + // If control is down, other platforms will not. + mouseDragged(evt); + } + int res = findRes(evt); int seq = findSeq(evt); + if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) return; @@ -342,225 +512,557 @@ public class SeqPanel extends JPanel if (res > sequence.getLength()) { - return; + return; + } + + if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) + { + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + } + + setStatusMessage(sequence, res, seq); + + // use aa to see if the mouse pointer is on a + if (av.showSequenceFeatures) + { + SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); + if(features!=null) + { + StringBuffer sbuffer = new StringBuffer(""); + StringBuffer seqSpecific = new StringBuffer(); + + for (int i = 0; i < features.length; i++) + { + + if ( (features[i].getBegin() <= sequence.findPosition(res)) && + (features[i].getEnd() >= sequence.findPosition(res))) + { + if(av.featuresDisplayed==null + || !av.featuresDisplayed.containsKey(features[i].getType())) + continue; + + + if (features[i].getType().equals("disulfide bond")) + { + if (features[i].getBegin() == sequence.findPosition(res) + || features[i].getEnd() == sequence.findPosition(res)) + { + if (sbuffer.length() > 6) + sbuffer.append("
"); + sbuffer.append("disulfide bond " + features[i].getBegin() + ":" + + features[i].getEnd()); + if (features[i].links != null) + sbuffer.append(" "); + } + } + else + { + if (sbuffer.length() > 6) + sbuffer.append("
"); + + sbuffer.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + sbuffer.append(" " + features[i].end); + + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) + sbuffer.append("; " + features[i].getDescription()); + + if (features[i].getValue("status") != null) + { + sbuffer.append("; (" + features[i].getValue("status") + ")"); + } + if (features[i].links != null) + sbuffer.append(" "); + + } + } + else if(features[i].begin==0 && features[i].end==0) + { + // seqSpecific.append(features[i].featureGroup+": " + // + features[i].getType()+" " + // +features[i].getDescription()+"
"); + + } + } + + if(seqSpecific.length()>0) + seqSpecific.setLength(seqSpecific.length()-4); + + sbuffer.append(seqSpecific); + sbuffer.append(""); + if(sbuffer.length()==13) // + setToolTipText(""); + else + setToolTipText(sbuffer.toString()); + } + else + setToolTipText(""); } + } - Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + - ""); - String aa = ""; + void setStatusMessage(SequenceI sequence, int res, int seq) + { + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); + Object obj = null; + if (av.alignment.isNucleotide()) + { + obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + + ""); if (obj != null) + text.append(" Nucleotide: "); + } + else + { + obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + if (obj != null) + text.append(" Residue: "); + } + + if (obj != null) + { + + if (obj != "") + { + text.append(obj + " (" + sequence.findPosition(res) + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); + + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseDragged(MouseEvent evt) + { + if (mouseWheelPressed) + { + int oldWidth = av.charWidth; + + //Which is bigger, left-right or up-down? + if (Math.abs(evt.getY() - lastMousePress.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++; + } + + if(fontSize<1) + fontSize = 1; + + av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); + av.charWidth = oldWidth; + ap.fontChanged(); + } + else { - aa = obj.toString(); + if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) + { + av.charWidth--; + } + else if (evt.getX() > lastMousePress.getX()) + { + av.charWidth++; + } + + ap.repaint(); } - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.charWidth; + + lastMousePress = evt.getPoint(); + + 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(); + + if(groupEditing && sg==null) + return; - if (aa != "") + if (!groupEditing && av.hasHiddenRows) { - text.append(" Residue: " + aa + " (" + - av.getAlignment().getSequenceAt(seq).findPosition(res) + ")"); + //This needs to check all the sequences in a group edit,m + // not just the startseq + if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) + { + groupEditing = true; + } } - ap.alignFrame.statusBar.setText(text.toString()); + SequenceI seq = av.alignment.getSequenceAt(startseq); + StringBuffer message = new StringBuffer(); + if (groupEditing) + message.append("Edit group:"); + else + message.append("Edit sequence: "+seq.getName()); - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) - { - Vector features = sequence.getSequenceFeatures(); - Enumeration e = features.elements(); - StringBuffer sbuffer = new StringBuffer(); + if(insertGap) + message.append(" insert "); + else + message.append(" delete "); - while (e.hasMoreElements()) - { - SequenceFeature sf = (SequenceFeature) e.nextElement(); + message.append(Math.abs(startres-lastres)+" gaps."); + ap.alignFrame.statusBar.setText(message.toString()); - if ((sf.getStart() <= sequence.findPosition(res)) && - (sf.getEnd() >= sequence.findPosition(res))) - { - if (sbuffer.length() > 0) - { - sbuffer.append("; "); - } - sbuffer.append(sf.getType() + " " + sf.getDescription()); + //Are we editing within a selection group? + if (groupEditing + || (sg != null && sg.sequences.contains(seq))) + { + fixedColumns = true; - if (sf.getStatus().length() > 0) - { - sbuffer.append(" (" + sf.getStatus() + ")"); - } - } - } + fixedLeft = sg.getStartRes(); + fixedRight = sg.getEndRes(); + + if ( (startres < fixedLeft && lastres >= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <=fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) + { + endEditing(); + return; + } - this.setToolTipText(sbuffer.toString()); + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } } - } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseDragged(MouseEvent evt) - { - // If we're dragging we're editing - int res = findRes(evt); - if (res < 0) - { - res = 0; - } - if ((lastres == -1) || (lastres == res)) + if(av.hasHiddenColumns) { - return; - } + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); - boolean dragRight = true; + if( ( insertGap && startres>y1 && lastresy2) ) + { + endEditing(); + return; + } - if ((res < av.getAlignment().getWidth()) && (res < lastres)) - { - dragRight = false; + if(fixedRightfixedLeft && fixedLeft==-1) + fixedLeft = y1; } - if (res != lastres) + if (groupEditing) { - // Group editing - if (groupEditing) + + /*if (av.hasHiddenRows) + { + //sg might be null as the user may only see 1 sequence + if (sg == null) { - SequenceGroup sg = av.getSelectionGroup(); + sg = new SequenceGroup(); + sg.addSequence(av.alignment.getSequenceAt(startseq), false); + } - if (sg == null) - { - lastres = -1; + SequenceGroup tmp = new SequenceGroup(); - return; - } + //Do any of the sequences have hidden associates? + for (int s = 0; s < sg.getSize(); s++) + { + seq = sg.getSequenceAt(s); + tmp.addSequence(seq, false); + if (seq.getHiddenSequences() != null) + { + for (int h = 0; h < seq.getHiddenSequences().getSize(); h++) + tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h), + false); + } + } + + sg = tmp; + }*/ + // int blankColumn = -1; - // drag to right - if (dragRight) + + // 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() + 1 == av.alignment.getWidth()) + { + sg.setEndRes(av.alignment.getWidth() + startres - lastres); + fixedRight = sg.getEndRes(); + } + + // Is it valid with fixed columns?? + // Find the next gap before the end + // of the visible region boundary + boolean blank = false; + for (fixedRight = fixedRight; + fixedRight > lastres; + fixedRight--) + { + blank = true; + for (int s = 0; s < sg.getSize(); s++) + { + seq = sg.getSequenceAt(s); + for (int j = 0; j < startres - lastres; j++) { - sg.setEndRes(sg.getEndRes() + (res - lastres)); + if (!jalview.util.Comparison.isGap( + seq.getCharAt(fixedRight - j))) + { + blank = false; + break; + } } + } + if (blank) + break; + } - // drag to left - else - { - /// Are we able to delete? - // ie are all columns blank? - boolean deleteAllowed = false; + if (!blank) + { + if(sg.getSize() == av.alignment.getHeight()) + { + //We can still insert gaps if the selectionGroup + //contains all the sequences + sg.setEndRes(sg.getEndRes()+startres-lastres); + fixedRight = av.alignment.getWidth()+startres-lastres; + } + else + { + endEditing(); + return; + } + } + } - for (int s = 0; s < sg.getSize(); s++) - { - SequenceI seq = sg.getSequenceAt(s); - - for (int j = res; j < lastres; j++) - { - if (seq.getSequence().length() <= j) - { - continue; - } - - if (!jalview.util.Comparison.isGap( - seq.getSequence().charAt(j))) - { - // Not a gap, block edit not valid - res = j + 1; - deleteAllowed = false; - - continue; - } - - deleteAllowed = true; - } - } - if (!deleteAllowed) - { - lastres = -1; + // drag to left + else if(!insertGap) + { + /// Are we able to delete? + // ie are all columns blank? - return; - } + for (int s = 0; s < sg.getSize(); s++) + { + seq = sg.getSequenceAt(s); - sg.setEndRes(sg.getEndRes() - (lastres - res)); + for (int j = startres; j < lastres; j++) + { + if (seq.getSequence().length() <= j) + { + continue; } - for (int i = 0; i < sg.getSize(); i++) + if (!jalview.util.Comparison.isGap( + seq.getSequence().charAt(j))) { - SequenceI s = sg.getSequenceAt(i); - int k = av.alignment.findIndex(s); + // Not a gap, block edit not valid + endEditing(); + return; + } + } + } + } - // drag to right - if (dragRight) - { - for (int j = lastres; j < res; j++) - { - insertChar(j, k); - } - } - // drag to left - else - { - for (int j = res; j < lastres; j++) - { - if (s.getLength() > j) - { - deleteChar(res, k); - } - } - } + for (int i = 0; i < sg.getSize(); i++) + { + seq = sg.getSequenceAt(i); + + if (insertGap) + { + // dragging to the right + for (int j = lastres; j < startres; j++) + { + if (fixedColumns && fixedRight != -1) + { + insertChar(j, seq, fixedRight); } + else + insertChar(j, seq); + } } - else /////Editing a single sequence/////////// + else { - if ((res < av.getAlignment().getWidth()) && (res > lastres)) + // dragging to the left + for (int j = lastres; j > startres; j--) + { + if (fixedColumns && fixedRight != -1) { - // dragging to the right - for (int j = lastres; j < res; j++) - { - insertChar(j, startseq); - } + deleteChar(startres, seq, fixedRight); } - else if ((res < av.getAlignment().getWidth()) && - (res < lastres)) + else { - // dragging to the left - for (int j = lastres; j > res; j--) - { - if (jalview.util.Comparison.isGap( - av.alignment.getSequenceAt(startseq) - .getSequence().charAt(res))) - { - deleteChar(res, startseq); - } - else - { - break; - } - } + deleteChar(startres, seq); + } + } + } + } + } + else /////Editing a single sequence/////////// + { + if (insertGap) + { + // dragging to the right + for (int j = lastres; j < startres; j++) + { + if (fixedColumns && fixedRight != -1) + { + if (sg.getStartRes() == 0 + && sg.getEndRes() + 1 == av.alignment.getWidth() + && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight))) + { + //Single sequence edit, whole sequence selected, + //extend the selection group + sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres); + fixedColumns = false; + insertChar(j, seq); } + else + insertChar(j, seq, fixedRight); + } + else + insertChar(j, seq); + } + } + else + { + // dragging to the left + for (int j = lastres; j > startres; j--) + { + if (fixedColumns && fixedRight != -1) + { + deleteChar(startres, seq, fixedRight); + } + else + { + deleteChar(startres, seq); + } } + } } - endEdit = res; - lastres = res; + lastres = startres; seqCanvas.repaint(); } + /** * DOCUMENT ME! * - * @param seqstart DOCUMENT ME! - * @param seqend DOCUMENT ME! - * @param start DOCUMENT ME! + * @param j DOCUMENT ME! + * @param seq DOCUMENT ME! */ - public void drawChars(int seqstart, int seqend, int start) + void insertChar(int j, SequenceI seq) { - seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, - seqend, av.getStartRes(), av.getStartSeq(), 0); - seqCanvas.repaint(); + seq.insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = true; + } + + void insertChar(int j, SequenceI seq, int fixedColumn) + { + //Find the next gap before the end of the visible region boundary + //If lastCol > j, theres a boundary after the gap insertion + int blankColumn = fixedColumn; + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } + } + + if (blankColumn <= j) + { + endEditing(); + return; + } + + if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + { + //Just Checking + System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn)); + return; + } + + seq.deleteCharAt(blankColumn); + seq.insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = true; + } + + void deleteChar(int j, SequenceI seq, int fixedColumn) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + { + ap.alignFrame.statusBar.setText( + "End editing: Tried removing residue " + seq.getCharAt(j)); + return; + } + + seq.deleteCharAt(j); + seq.insertCharAt(fixedColumn, av.getGapCharacter()); + seqEditOccurred = true; } /** @@ -569,40 +1071,102 @@ public class SeqPanel extends JPanel * @param j DOCUMENT ME! * @param seq DOCUMENT ME! */ - public void insertChar(int j, int seq) + void deleteChar(int j, SequenceI seq) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + { + ap.alignFrame.statusBar.setText( + "End editing: Tried removing residue " + seq.getCharAt(j)); + return; + } + + seq.deleteCharAt(j); + seqEditOccurred = true; + seqCanvas.repaint(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) { - av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = seq; + if(oldSeq < 0) + oldSeq = 0; + + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } } /** * DOCUMENT ME! * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! + * @param e DOCUMENT ME! */ - public void deleteChar(int j, int seq) + public void mouseExited(MouseEvent e) { - av.alignment.getSequenceAt(seq).deleteCharAt(j); - seqEditOccurred = seq; + if (av.getWrapAlignment()) + { + return; + } + + if (mouseDragging) + { + scrollThread = new ScrollThread(); + } + } + + public void mouseClicked(MouseEvent evt) + {} + + 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); + } - av.alignment.getWidth(); - seqCanvas.repaint(); } + + /** * DOCUMENT ME! * * @param i DOCUMENT ME! */ - void editOccurred(int i) + void editOccurred() { - if (endEdit == startEdit) + if (!seqEditOccurred) { ap.alignFrame.historyList.pop(); ap.alignFrame.updateEditMenuBar(); } + endEditing(); + av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); } @@ -626,13 +1190,12 @@ public class SeqPanel extends JPanel "Cannot edit annotations in wrapped view.", "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE); - return; + return; } if(seq<0 || res<0) return; - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) @@ -672,57 +1235,83 @@ public class SeqPanel extends JPanel (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; - av.setSelectionGroup(stretchGroup); - break; } } } + + av.setSelectionGroup(stretchGroup); + } - if (stretchGroup == null) + if (av.cursorMode) { - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, - av.getGlobalColourScheme(), "Background"); - } - if (av.getAbovePIDThreshold()) + 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++) { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); + 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()); } - else if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + else if (stretchGroup == null) { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null); - pop.show(this, evt.getX(), evt.getY()); + //Only if left mouse button do we want to change group sizes - // edit the properties of existing group - } + // 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 != null) && (stretchGroup.getEndRes() == res)) - { + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), + "Background"); + } + + 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)) - { + } + else if ( (stretchGroup != null) && + (stretchGroup.getStartRes() == res)) + { // Edit end res position of selected group changeStartRes = true; + } + stretchGroup.getWidth(); } - stretchGroup.getWidth(); - seqCanvas.repaint(); } @@ -733,17 +1322,12 @@ public class SeqPanel extends JPanel */ public void doMouseReleasedDefineMode(MouseEvent evt) { - if (mouseDragging) - { - stretchGroup.recalcConservation(); - mouseDragging = false; - } - if (stretchGroup == null) { return; } + if(stretchGroup.cs!=null) { if (stretchGroup.cs instanceof ClustalxColourScheme) @@ -757,6 +1341,7 @@ public class SeqPanel extends JPanel { SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); + stretchGroup.recalcConservation(); } else { @@ -783,14 +1368,19 @@ public class SeqPanel extends JPanel if(wrappedBlock!=startWrapBlock) return; - if (stretchGroup == null) - { + if (stretchGroup == null) + { return; - } + } - if (res > av.alignment.getWidth()) + + if(y > av.alignment.getHeight()) + { + y = av.alignment.getHeight() -1; + } + if(res> av.alignment.getWidth()) { - res = av.alignment.getWidth() - 1; + res = av.alignment.getWidth()-1; } if (stretchGroup.getEndRes() == res) @@ -808,10 +1398,6 @@ public class SeqPanel extends JPanel { res = av.getStartRes(); } - else if (res > av.getEndRes() && !av.getWrapAlignment()) - { - res = av.getEndRes(); - } if (changeEndRes) { @@ -839,7 +1425,8 @@ public class SeqPanel extends JPanel dragDirection = -1; } - while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight())) + + while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) { // This routine ensures we don't skip any sequences, as the // selection is quite slow. @@ -847,6 +1434,9 @@ public class SeqPanel extends JPanel oldSeq += dragDirection; + if(oldSeq<0) + break; + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); if (stretchGroup.sequences.contains(nextSeq)) @@ -864,7 +1454,9 @@ public class SeqPanel extends JPanel } } - oldSeq = y; + if(oldSeq < 0) + oldSeq = -1; + mouseDragging = true; if (scrollThread != null) @@ -875,37 +1467,29 @@ public class SeqPanel extends JPanel seqCanvas.repaint(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void doMouseEnteredDefineMode(MouseEvent e) + void scrollCanvas(MouseEvent evt) { - if (scrollThread != null) + if(evt==null) + { + if(scrollThread!=null) { - scrollThread.running = false; + scrollThread.running = false; + scrollThread = null; } - } + mouseDragging = false; + } + else + { + if (scrollThread == null) + scrollThread = new ScrollThread(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void doMouseExitedDefineMode(MouseEvent e) - { - if (av.getWrapAlignment()) - { - return; - } + mouseDragging = true; + scrollThread.setEvent(evt); + } - if (mouseDragging) - { - scrollThread = new ScrollThread(); - } } + // this class allows scrolling off the bottom of the visible alignment class ScrollThread extends Thread { @@ -949,17 +1533,17 @@ public class SeqPanel extends JPanel if (mouseDragging && (evt.getX() < 0)) { - running = ap.scrollRight(true); + running = ap.scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = ap.scrollRight(false); + running = ap.scrollRight(true); } } try { - Thread.sleep(75); + Thread.sleep(20); } catch (Exception ex) {