X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=126d755212f545bbc975941771e0c01f40094ef8;hb=a853fae4d9d4dbc80e877741c017fca7ee80c59e;hp=4d5b080f0dfc400d44e8232da5ec67c07d7e773a;hpb=f7411d1acf9235d91fb5e9adb1e0e3d36f44c861;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 4d5b080..126d755 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.*; @@ -27,8 +25,6 @@ import jalview.schemes.*; import java.awt.*; import java.awt.event.*; -import java.util.*; - import javax.swing.*; @@ -38,7 +34,9 @@ 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 +45,10 @@ 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 +65,10 @@ public class SeqPanel extends JPanel SequenceGroup stretchGroup = null; boolean remove = false; + Point lastMousePress; boolean mouseWheelPressed = false; + StringBuffer keyboardNo1; + StringBuffer keyboardNo2; /** * Creates a new SeqPanel object. @@ -91,177 +90,359 @@ public class SeqPanel extends JPanel ap = p; - addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { - if (av.getWrapAlignment()) - { - return; - } + if(!av.isDataset()) + { + addMouseMotionListener(this); + addMouseListener(this); + addMouseWheelListener(this); + } + } - doMouseMoved(evt); - } + int startWrapBlock=-1; + int wrappedBlock=-1; + int findRes(MouseEvent evt) + { + int res = 0; + int x = evt.getX(); - public void mouseDragged(MouseEvent evt) - { - if (av.getWrapAlignment()) - { - return; - } + if (av.wrapAlignment) + { - if (editingSeqs) - { - doMouseDragged(evt); - } - else - { - doMouseDraggedDefineMode(evt); - } - } - }); + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - 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(); - ap.repaint(); - - } - else - { - if (e.getWheelRotation() > 0) - ap.scrollUp(false); - else - ap.scrollUp(true); - } - - } - }); - - - addMouseListener(new MouseAdapter() - { - public void mouseReleased(MouseEvent evt) - { - mouseWheelPressed = false; - if (av.getWrapAlignment()) - { - return; - } + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); - if (editingSeqs) - { - doMouseReleased(evt); - } - else - { - doMouseReleasedDefineMode(evt); - } - } + int y = evt.getY(); + y -= hgap; + x -= seqCanvas.LABEL_WEST; - public void mousePressed(MouseEvent evt) - { - if( javax.swing.SwingUtilities.isMiddleMouseButton(evt)) - { - mouseWheelPressed = true; - return; - } - if (av.getWrapAlignment()) - { - return; - } - if (evt.isShiftDown() || evt.isAltDown() || - evt.isControlDown()) - { - if (evt.isAltDown() || evt.isControlDown()) - { - groupEditing = true; - } + int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); - editingSeqs = true; - doMousePressed(evt); - } - else - { - doMousePressedDefineMode(evt); - } - } + wrappedBlock = y / cHeight; + wrappedBlock += av.getStartRes() / cwidth; - public void mouseExited(MouseEvent evt) - { - if (av.getWrapAlignment() || editingSeqs) - { - return; - } + res = wrappedBlock * cwidth + x / av.getCharWidth(); - doMouseExitedDefineMode(evt); - } + } + else + { + res = (x / av.getCharWidth()) + av.getStartRes(); + } - public void mouseEntered(MouseEvent evt) - { - if (av.getWrapAlignment() || editingSeqs) - { - return; - } + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); - doMouseEnteredDefineMode(evt); - } - }); + return res; + + } + + int findSeq(MouseEvent evt) + { + + int seq = 0; + int y = evt.getY(); + + if (av.wrapAlignment) + { + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; + + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); + + y -= hgap; + + seq = ( (y % cHeight) / av.getCharHeight()); + } + else + { + seq = (y / av.getCharHeight()) + av.getStartSeq(); + } + + return seq; + } + + 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; + + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } - startseq = -1; - lastres = -1; - seqEditOccurred = -1; - editingSeqs = false; - groupEditing = false; + 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(); - int seq; - int res; + if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + { + mouseWheelPressed = true; + return; + } - int x = evt.getX(); - int y = evt.getY(); + if (evt.isShiftDown() || evt.isAltDown() || + evt.isControlDown()) + { + if (evt.isAltDown() || evt.isControlDown()) + { + groupEditing = true; + } + editingSeqs = true; + } + else + { + doMousePressedDefineMode(evt); + return; + } - res = (x / av.getCharWidth()) + av.getStartRes(); - seq = (y / av.getCharHeight()) + av.getStartSeq(); + + + int seq = findSeq(evt); + int res = findRes(evt); + + 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())) @@ -275,9 +456,6 @@ public class SeqPanel extends JPanel lastres = -1; } - startEdit = lastres; - endEdit = lastres; - return; } @@ -286,93 +464,130 @@ public class SeqPanel extends JPanel * * @param evt DOCUMENT ME! */ - public void doMouseMoved(MouseEvent evt) + public void mouseMoved(MouseEvent evt) { - int res = 0; - int seq = 0; - int x = evt.getX(); - int y = evt.getY(); - - if (av.wrapAlignment) - { - y -= (2 * av.charHeight); + if (editingSeqs) + { + // This is because MacOSX creates a mouseMoved + // If control is down, other platforms will not. + mouseDragged(evt); + } - int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; + int res = findRes(evt); + int seq = findSeq(evt); - res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) + - (x / av.getCharWidth()) + av.getStartRes(); - y %= chunkHeight; - seq = (y / av.getCharHeight()) + av.getStartSeq(); - } - else - { - res = (x / av.getCharWidth()) + av.getStartRes(); - seq = (y / av.getCharHeight()) + av.getStartSeq(); - } - - if (seq >= av.getAlignment().getHeight()) - { + if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) return; - } - SequenceI sequence = av.getAlignment().getSequenceAt(seq); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if (res > sequence.getLength()) - { - return; - } - - Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + - ""); - String aa = ""; - - if (obj != null) - { - aa = obj.toString(); - } + if (res > sequence.getLength()) + { + return; + } - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); + if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) + { + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + } - if (aa != "") - { - text.append(" Residue: " + aa + " (" + - av.getAlignment().getSequenceAt(seq).findPosition(res) + ")"); - } - - ap.alignFrame.statusBar.setText(text.toString()); + setStatusMessage(sequence, res, seq); // 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(); - - while (e.hasMoreElements()) + SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); + if(features!=null) { - SequenceFeature sf = (SequenceFeature) e.nextElement(); + StringBuffer sbuffer = new StringBuffer(""); - if ((sf.getStart() <= sequence.findPosition(res)) && - (sf.getEnd() >= sequence.findPosition(res))) + for (int i = 0; i < features.length; i++) + { + + if ( (features[i].getBegin() <= sequence.findPosition(res)) && + (features[i].getEnd() >= sequence.findPosition(res))) { - if (sbuffer.length() > 0) + 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)) { - sbuffer.append("; "); + if (sbuffer.length() > 6) + sbuffer.append("
"); + sbuffer.append("disulfide bond " + features[i].getBegin() + ":" + + features[i].getEnd()); } + } + else + { + if (sbuffer.length() > 6) + sbuffer.append("
"); + if(features[i].featureGroup!=null) + sbuffer.append(features[i].featureGroup+";"); + + sbuffer.append(features[i].getType()); - sbuffer.append(sf.getType() + " " + sf.getDescription()); + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) + sbuffer.append("; " + features[i].getDescription()); - if (sf.getStatus().length() > 0) + if (features[i].getStatus() != null && features[i].getStatus().length()>0) { - sbuffer.append(" (" + sf.getStatus() + ")"); + sbuffer.append("; (" + features[i].getStatus() + ")"); } + } } + + } + + sbuffer.append(""); + if(sbuffer.length()==13) // + setToolTipText(""); + else + setToolTipText(sbuffer.toString()); } + else + setToolTipText(""); + } + } - this.setToolTipText(sbuffer.toString()); + 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()); + } /** @@ -380,10 +595,63 @@ public class SeqPanel extends JPanel * * @param evt DOCUMENT ME! */ - public void doMouseDragged(MouseEvent evt) + public void mouseDragged(MouseEvent evt) { - // If we're dragging we're editing - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + 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 + { + 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; + + lastMousePress = evt.getPoint(); + + return; + } + + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } + + int res = findRes(evt); if (res < 0) { @@ -395,150 +663,361 @@ public class SeqPanel extends JPanel return; } - boolean dragRight = true; + 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 (!groupEditing && av.hasHiddenRows) + { + //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; + } + } + + SequenceI seq = av.alignment.getSequenceAt(startseq); + StringBuffer message = new StringBuffer(); + if (groupEditing) + message.append("Edit group:"); + else + message.append("Edit sequence: "+seq.getName()); + + 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.sequences.contains(seq))) + { + fixedColumns = true; + + 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; + } + + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } + } + + - if ((res < av.getAlignment().getWidth()) && (res < lastres)) + if(av.hasHiddenColumns) { - dragRight = false; + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + + if( ( insertGap && startres>y1 && lastresy2) ) + { + endEditing(); + return; + } + + 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); + } + } - // drag to right - if (dragRight) + sg = tmp; + }*/ + // int blankColumn = -1; + + + // 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; } /** @@ -547,80 +1026,104 @@ 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) { - av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = 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 j DOCUMENT ME! - * @param seq DOCUMENT ME! + * @param e DOCUMENT ME! */ - public void deleteChar(int j, int seq) + public void mouseEntered(MouseEvent e) { - av.alignment.getSequenceAt(seq).deleteCharAt(j); - seqEditOccurred = seq; + if(oldSeq < 0) + oldSeq = 0; - av.alignment.getWidth(); - seqCanvas.repaint(); + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } } /** * DOCUMENT ME! * - * @param i DOCUMENT ME! + * @param e DOCUMENT ME! */ - void editOccurred(int i) + public void mouseExited(MouseEvent e) { - if (endEdit == startEdit) + if (av.getWrapAlignment()) { - ap.alignFrame.historyList.pop(); - ap.alignFrame.updateEditMenuBar(); + return; } - av.updateConservation(); - av.updateConsensus(); - - // Y O Y CLUSTALX - ColourSchemeI cs = av.getGlobalColourScheme(); - - if (av.getSelectionGroup() != null) + if (mouseDragging) { - av.getSelectionGroup().recalcConservation(); + scrollThread = new ScrollThread(); } + } - if (cs.conservationApplied()) - { - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, av.alignment.getSequences(), - 0, av.alignment.getWidth() - 1); - c.calculate(); - c.verdict(false, av.ConsPercGaps); + public void mouseClicked(MouseEvent evt) + {} - if (cs instanceof ClustalxColourScheme) - { - ClustalxColourScheme cxs = (ClustalxColourScheme) cs; - cxs.resetClustalX(av.alignment.getSequences(), - av.alignment.getWidth()); - cs.setConservation(c); - av.setGlobalColourScheme(cs); - } - else - { - cs.setConservation(c); - av.setGlobalColourScheme(cs); - } - } + 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); + } + + } + + + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + */ + void editOccurred() + { + if (!seqEditOccurred) + { + ap.alignFrame.historyList.pop(); + ap.alignFrame.updateEditMenuBar(); + } + + endEditing(); + + av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); - if (cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(), - av.alignment.getWidth()); - av.setGlobalColourScheme(cs); - } } /** @@ -630,9 +1133,23 @@ public class SeqPanel extends JPanel */ public void doMousePressedDefineMode(MouseEvent evt) { - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq(); - oldSeq = seq; + int res = findRes(evt); + int seq = findSeq(evt); + oldSeq = seq; + + 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; + } + + if(seq<0 || res<0) + return; SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); @@ -681,6 +1198,15 @@ public class SeqPanel extends JPanel } } + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } + + if (stretchGroup == null) { // define a new group here @@ -734,17 +1260,12 @@ 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) @@ -758,6 +1279,7 @@ public class SeqPanel extends JPanel { SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); + stretchGroup.recalcConservation(); } else { @@ -778,17 +1300,25 @@ public class SeqPanel extends JPanel */ public void doMouseDraggedDefineMode(MouseEvent evt) { - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq(); + int res = findRes(evt); + int y = findSeq(evt); - if (stretchGroup == null) - { + if(wrappedBlock!=startWrapBlock) + return; + + 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) @@ -806,10 +1336,6 @@ public class SeqPanel extends JPanel { res = av.getStartRes(); } - else if (res > av.getEndRes()) - { - res = av.getEndRes(); - } if (changeEndRes) { @@ -837,7 +1363,8 @@ 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. @@ -845,6 +1372,9 @@ public class SeqPanel extends JPanel oldSeq += dragDirection; + if(oldSeq<0) + break; + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); if (stretchGroup.sequences.contains(nextSeq)) @@ -862,7 +1392,9 @@ public class SeqPanel extends JPanel } } - oldSeq = y; + if(oldSeq < 0) + oldSeq = -1; + mouseDragging = true; if (scrollThread != null) @@ -873,37 +1405,29 @@ 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 { @@ -947,17 +1471,17 @@ 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) {