X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=f28217d03726c2f3943b816be85fa1cebef43177;hb=5a631296dd1dcc1df7b50487a647c27333696c74;hp=e3cf330766f016c35f7b0cfd43975dabf2845c75;hpb=9ba5a485b66e9c5a86b12dedc7b32616f3ef6db8;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index e3cf330..f28217d 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -20,14 +20,34 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Point; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.MouseWheelEvent; +import java.awt.event.MouseWheelListener; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; + +import javax.swing.JPanel; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; + import jalview.api.AlignViewportI; import jalview.bin.Cache; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; @@ -48,25 +68,8 @@ import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; - -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Point; -import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; -import java.awt.event.MouseMotionListener; -import java.awt.event.MouseWheelEvent; -import java.awt.event.MouseWheelListener; -import java.util.ArrayList; -import java.util.Collections; -import java.util.List; -import java.util.ListIterator; - -import javax.swing.JPanel; -import javax.swing.SwingUtilities; -import javax.swing.ToolTipManager; +import jalview.viewmodel.ViewportRanges; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; /** * DOCUMENT ME! @@ -74,20 +77,100 @@ import javax.swing.ToolTipManager; * @author $author$ * @version $Revision: 1.130 $ */ -public class SeqPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener, SequenceListener, - SelectionListener - +public class SeqPanel extends JPanel + implements MouseListener, MouseMotionListener, MouseWheelListener, + SequenceListener, SelectionListener { - /** DOCUMENT ME!! */ + /* + * a class that holds computed mouse position + * - column of the alignment (0...) + * - sequence offset (0...) + * - annotation row offset (0...) + * where annotation offset is -1 unless the alignment is shown + * in wrapped mode, annotations are shown, and the mouse is + * over an annnotation row + */ + static class MousePos + { + /* + * alignment column position of cursor (0...) + */ + final int column; + + /* + * index in alignment of sequence under cursor, + * or nearest above if cursor is not over a sequence + */ + final int seqIndex; + + /* + * index in annotations array of annotation under the cursor + * (only possible in wrapped mode with annotations shown), + * or -1 if cursor is not over an annotation row + */ + final int annotationIndex; + + MousePos(int col, int seq, int ann) + { + column = col; + seqIndex = seq; + annotationIndex = ann; + } + + boolean isOverAnnotation() + { + return annotationIndex != -1; + } + + @Override + public boolean equals(Object obj) + { + if (obj == null || !(obj instanceof MousePos)) + { + return false; + } + MousePos o = (MousePos) obj; + boolean b = (column == o.column && seqIndex == o.seqIndex + && annotationIndex == o.annotationIndex); + // System.out.println(obj + (b ? "= " : "!= ") + this); + return b; + } + + /** + * A simple hashCode that ensures that instances that satisfy equals() have + * the same hashCode + */ + @Override + public int hashCode() + { + return column + seqIndex + annotationIndex; + } + + /** + * toString method for debug output purposes only + */ + @Override + public String toString() + { + return String.format("c%d:s%d:a%d", column, seqIndex, + annotationIndex); + } + } + + private static final int MAX_TOOLTIP_LENGTH = 300; + public SeqCanvas seqCanvas; - /** DOCUMENT ME!! */ public AlignmentPanel ap; - protected int lastres; + /* + * last position for mouseMoved event + */ + private MousePos lastMousePosition; + + protected int editLastRes; - protected int startseq; + protected int editStartSeq; protected AlignViewport av; @@ -124,8 +207,6 @@ public class SeqPanel extends JPanel implements MouseListener, StringBuffer keyboardNo2; - java.net.URL linkImageURL; - private final SequenceAnnotationReport seqARep; StringBuilder tooltipText = new StringBuilder(); @@ -139,35 +220,32 @@ public class SeqPanel extends JPanel implements MouseListener, SearchResultsI lastSearchResults; /** - * Creates a new SeqPanel object. + * Creates a new SeqPanel object * - * @param avp - * DOCUMENT ME! - * @param p - * DOCUMENT ME! + * @param viewport + * @param alignPanel */ - public SeqPanel(AlignViewport av, AlignmentPanel ap) + public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { - linkImageURL = getClass().getResource("/images/link.gif"); - seqARep = new SequenceAnnotationReport(linkImageURL.toString()); + seqARep = new SequenceAnnotationReport(true); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = av; + this.av = viewport; setBackground(Color.white); - seqCanvas = new SeqCanvas(ap); + seqCanvas = new SeqCanvas(alignPanel); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); - this.ap = ap; + this.ap = alignPanel; - if (!av.isDataset()) + if (!viewport.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = av.getStructureSelectionManager(); + ssm = viewport.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@ -178,6 +256,73 @@ public class SeqPanel extends JPanel implements MouseListener, int wrappedBlock = -1; /** + * Computes the column and sequence row (and possibly annotation row when in + * wrapped mode) for the given mouse position + * + * @param evt + * @return + */ + MousePos findMousePosition(MouseEvent evt) + { + int col = findColumn(evt); + int seqIndex = -1; + int annIndex = -1; + int y = evt.getY(); + + int charHeight = av.getCharHeight(); + int alignmentHeight = av.getAlignment().getHeight(); + if (av.getWrapAlignment()) + { + seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(), + seqCanvas.getHeight()); + + /* + * yPos modulo height of repeating width + */ + int yOffsetPx = y % seqCanvas.wrappedRepeatHeightPx; + + /* + * height of sequences plus space / scale above, + * plus gap between sequences and annotations + */ + int alignmentHeightPixels = seqCanvas.wrappedSpaceAboveAlignment + + alignmentHeight * charHeight + + SeqCanvas.SEQS_ANNOTATION_GAP; + if (yOffsetPx >= alignmentHeightPixels) + { + /* + * mouse is over annotations; find annotation index, also set + * last sequence above (for backwards compatible behaviour) + */ + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + int rowOffsetPx = yOffsetPx - alignmentHeightPixels; + annIndex = AnnotationPanel.getRowIndex(rowOffsetPx, anns); + seqIndex = alignmentHeight - 1; + } + else + { + /* + * mouse is over sequence (or the space above sequences) + */ + yOffsetPx -= seqCanvas.wrappedSpaceAboveAlignment; + if (yOffsetPx >= 0) + { + seqIndex = Math.min(yOffsetPx / charHeight, alignmentHeight - 1); + } + } + } + else + { + ViewportRanges ranges = av.getRanges(); + seqIndex = Math.min((y / charHeight) + ranges.getStartSeq(), + alignmentHeight - 1); + seqIndex = Math.min(seqIndex, ranges.getEndSeq()); + } + + return new MousePos(col, seqIndex, annIndex); + } + /** * Returns the aligned sequence position (base 0) at the mouse position, or * the closest visible one * @@ -189,10 +334,11 @@ public class SeqPanel extends JPanel implements MouseListener, int res = 0; int x = evt.getX(); - int startRes = av.getRanges().getStartRes(); + final int startRes = av.getRanges().getStartRes(); + final int charWidth = av.getCharWidth(); + if (av.getWrapAlignment()) { - int hgap = av.getCharHeight(); if (av.getScaleAboveWrapped()) { @@ -203,78 +349,50 @@ public class SeqPanel extends JPanel implements MouseListener, + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); - y -= hgap; - x = Math.max(0, x - seqCanvas.LABEL_WEST); + y = Math.max(0, y - hgap); + x -= seqCanvas.getLabelWidthWest(); + if (x < 0) + { + // mouse is over left scale + return -1; + } int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) { return 0; } + if (x >= cwidth * charWidth) + { + // mouse is over right scale + return -1; + } wrappedBlock = y / cHeight; wrappedBlock += startRes / cwidth; // allow for wrapped view scrolled right (possible from Overview) int startOffset = startRes % cwidth; - res = wrappedBlock * cwidth - + Math.min(cwidth - 1, startOffset + x / av.getCharWidth()); + res = wrappedBlock * cwidth + startOffset + + Math.min(cwidth - 1, x / charWidth); } else { - if (x > seqCanvas.getX() + seqCanvas.getWidth()) - { - // make sure we calculate relative to visible alignment, rather than - // right-hand gutter - x = seqCanvas.getX() + seqCanvas.getWidth(); - } - res = (x / av.getCharWidth()) + startRes; - if (res > av.getRanges().getEndRes()) - { - // moused off right - res = av.getRanges().getEndRes(); - } + /* + * make sure we calculate relative to visible alignment, + * rather than right-hand gutter + */ + x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth()); + res = (x / charWidth) + startRes; + res = Math.min(res, av.getRanges().getEndRes()); } if (av.hasHiddenColumns()) { res = av.getAlignment().getHiddenColumns() - .adjustForHiddenColumns(res); + .visibleToAbsoluteColumn(res); } return res; - - } - - int findSeq(MouseEvent evt) - { - int seq = 0; - int y = evt.getY(); - - if (av.getWrapAlignment()) - { - int hgap = av.getCharHeight(); - if (av.getScaleAboveWrapped()) - { - hgap += av.getCharHeight(); - } - - int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap + seqCanvas.getAnnotationHeight(); - - y -= hgap; - - seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() - .getHeight() - 1); - } - else - { - seq = Math.min((y / av.getCharHeight()) - + av.getRanges().getStartSeq(), - av - .getAlignment().getHeight() - 1); - } - - return seq; } /** @@ -288,16 +406,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (editCommand != null && editCommand.getSize() > 0) { ap.alignFrame.addHistoryItem(editCommand); - av.firePropertyChange("alignment", null, av.getAlignment() - .getSequences()); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); } } finally { /* * Tidy up come what may... */ - startseq = -1; - lastres = -1; + editStartSeq = -1; + editLastRes = -1; editingSeqs = false; groupEditing = false; keyboardNo1 = null; @@ -309,13 +427,13 @@ public class SeqPanel extends JPanel implements MouseListener, void setCursorRow() { seqCanvas.cursorY = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorColumn() { seqCanvas.cursorX = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorRowAndColumn() @@ -328,7 +446,7 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX = getKeyboardNo1() - 1; seqCanvas.cursorY = getKeyboardNo2() - 1; - scrollToVisible(); + scrollToVisible(true); } } @@ -337,7 +455,7 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; - scrollToVisible(); + scrollToVisible(true); } void moveCursor(int dx, int dy) @@ -347,16 +465,30 @@ public class SeqPanel extends JPanel implements MouseListener, HiddenColumns hidden = av.getAlignment().getHiddenColumns(); - if (av.hasHiddenColumns() - && !hidden.isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); - while (!hidden.isVisible(seqCanvas.cursorX) - && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) + if (!hidden.isVisible(seqCanvas.cursorX)) { - seqCanvas.cursorX += dx; + int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx); + int[] region = hidden.getRegionWithEdgeAtRes(visx); + + if (region != null) // just in case + { + if (dx == 1) + { + // moving right + seqCanvas.cursorX = region[1] + 1; + } + else if (dx == -1) + { + // moving left + seqCanvas.cursorX = region[0] - 1; + } + } + seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX; } if (seqCanvas.cursorX >= maxWidth @@ -366,10 +498,16 @@ public class SeqPanel extends JPanel implements MouseListener, } } - scrollToVisible(); + scrollToVisible(false); } - void scrollToVisible() + /** + * Scroll to make the cursor visible in the viewport. + * + * @param jump + * just jump to the location rather than scrolling + */ + void scrollToVisible(boolean jump) { if (seqCanvas.cursorX < 0) { @@ -390,20 +528,44 @@ public class SeqPanel extends JPanel implements MouseListener, } endEditing(); - if (av.getWrapAlignment()) + + boolean repaintNeeded = true; + if (jump) { - av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); + // only need to repaint if the viewport did not move, as otherwise it will + // get a repaint + repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX, + seqCanvas.cursorY); } else { - av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY); + if (av.getWrapAlignment()) + { + // scrollToWrappedVisible expects x-value to have hidden cols subtracted + int x = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(seqCanvas.cursorX); + av.getRanges().scrollToWrappedVisible(x); + } + else + { + av.getRanges().scrollToVisible(seqCanvas.cursorX, + seqCanvas.cursorY); + } } - setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), + + if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX)) + { + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); + } - seqCanvas.repaint(); + if (repaintNeeded) + { + seqCanvas.repaint(); + } } + void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); @@ -474,15 +636,15 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(sg); } - ap.paintAlignment(false); + ap.paintAlignment(false, false); av.sendSelection(); } void insertGapAtCursor(boolean group) { groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX; editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -490,8 +652,8 @@ public class SeqPanel extends JPanel implements MouseListener, void deleteGapAtCursor(boolean group) { groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX + getKeyboardNo1(); + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX + getKeyboardNo1(); editSequence(false, false, seqCanvas.cursorX); endEditing(); } @@ -500,8 +662,8 @@ public class SeqPanel extends JPanel implements MouseListener, { // TODO not called - delete? groupEditing = group; - startseq = seqCanvas.cursorY; - lastres = seqCanvas.cursorX; + editStartSeq = seqCanvas.cursorY; + editLastRes = seqCanvas.cursorX; editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -566,24 +728,31 @@ public class SeqPanel extends JPanel implements MouseListener, @Override public void mouseReleased(MouseEvent evt) { + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } + boolean didDrag = mouseDragging; // did we come here after a drag mouseDragging = false; mouseWheelPressed = false; if (evt.isPopupTrigger()) // Windows: mouseReleased { - showPopupMenu(evt); + showPopupMenu(evt, pos); evt.consume(); return; } - if (!editingSeqs) + if (editingSeqs) + { + endEditing(); + } + else { doMouseReleasedDefineMode(evt, didDrag); - return; } - - endEditing(); } /** @@ -596,6 +765,11 @@ public class SeqPanel extends JPanel implements MouseListener, public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) + { + return; + } if (SwingUtilities.isMiddleMouseButton(evt)) { @@ -614,28 +788,23 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - doMousePressedDefineMode(evt); + doMousePressedDefineMode(evt, pos); return; } - int seq = findSeq(evt); - int res = findColumn(evt); - - if (seq < 0 || res < 0) - { - return; - } + int seq = pos.seqIndex; + int res = pos.column; if ((seq < av.getAlignment().getHeight()) && (res < av.getAlignment().getSequenceAt(seq).getLength())) { - startseq = seq; - lastres = res; + editStartSeq = seq; + editLastRes = res; } else { - startseq = -1; - lastres = -1; + editStartSeq = -1; + editLastRes = -1; } return; @@ -663,14 +832,16 @@ public class SeqPanel extends JPanel implements MouseListener, * the start of the highlighted region. */ @Override - public void highlightSequence(SearchResultsI results) + public String highlightSequence(SearchResultsI results) { if (results == null || results.equals(lastSearchResults)) { - return; + return null; } lastSearchResults = results; + boolean wasScrolled = false; + if (av.isFollowHighlight()) { // don't allow highlight of protein/cDNA to also scroll a complementary @@ -678,14 +849,90 @@ public class SeqPanel extends JPanel implements MouseListener, // over residue to change abruptly, causing highlighted residue in panel 2 // to change, causing a scroll in panel 1 etc) ap.setToScrollComplementPanel(false); - if (ap.scrollToPosition(results, false)) + wasScrolled = ap.scrollToPosition(results); + if (wasScrolled) { seqCanvas.revalidate(); } ap.setToScrollComplementPanel(true); } - setStatusMessage(results); - seqCanvas.highlightSearchResults(results); + + boolean noFastPaint = wasScrolled && av.getWrapAlignment(); + if (seqCanvas.highlightSearchResults(results, noFastPaint)) + { + setStatusMessage(results); + } + return results.isEmpty() ? null : getHighlightInfo(results); + } + + /** + * temporary hack: answers a message suitable to show on structure hover + * label. This is normally null. It is a peptide variation description if + *
+ * Sequence 3 ID: FER1_SOLLC + * Sequence 5 ID: FER1_PEA Residue: THR (4) + * Sequence 5 ID: FER1_PEA Residue: B (3) + * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2) + *+ * + * @param sequence + * @param seqIndex + * sequence position in the alignment (1..) + * @param sequenceChar + * the character under the cursor + * @param residuePos + * the sequence residue position (if not over a gap) + */ + protected void setStatusMessage(SequenceI sequence, int seqIndex, + char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); /* * Sequence number (if known), and sequence name. */ - String seqno = seq == -1 ? "" : " " + (seq + 1); + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") .append(sequence.getName()); @@ -905,31 +1240,28 @@ public class SeqPanel extends JPanel implements MouseListener, /* * Try to translate the display character to residue name (null for gap). */ - final String displayChar = String.valueOf(sequence.getCharAt(column)); - boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); - int pos = sequence.findPosition(column); + boolean isGapped = Comparison.isGap(sequenceChar); if (!isGapped) { boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); if (nucleotide) { residue = ResidueProperties.nucleotideName.get(displayChar); } else { - residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" - .equals(displayChar) ? "STOP" - : ResidueProperties.aa2Triplet.get(displayChar)); + residue = "X".equalsIgnoreCase(displayChar) ? "X" + : ("*".equals(displayChar) ? "STOP" + : ResidueProperties.aa2Triplet.get(displayChar)); } text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") .append(": ").append(residue == null ? displayChar : residue); - text.append(" (").append(Integer.toString(pos)).append(")"); + text.append(" (").append(Integer.toString(residuePos)).append(")"); } - ap.alignFrame.statusBar.setText(text.toString()); - - return pos; + ap.alignFrame.setStatus(text.toString()); } /** @@ -957,12 +1289,9 @@ public class SeqPanel extends JPanel implements MouseListener, if (seq == ds) { - /* - * Convert position in sequence (base 1) to sequence character array - * index (base 0) - */ - int start = m.getStart() - m.getSequence().getStart(); - setStatusMessage(seq, start, sequenceIndex); + int start = m.getStart(); + setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), + start); return; } } @@ -974,6 +1303,12 @@ public class SeqPanel extends JPanel implements MouseListener, @Override public void mouseDragged(MouseEvent evt) { + MousePos pos = findMousePosition(evt); + if (pos.isOverAnnotation() || pos.column == -1) + { + return; + } + if (mouseWheelPressed) { boolean inSplitFrame = ap.av.getCodingComplement() != null; @@ -982,8 +1317,8 @@ public class SeqPanel extends JPanel implements MouseListener, int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? - if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt - .getX() - lastMousePress.getX())) + if (Math.abs(evt.getY() - lastMousePress.getY()) > Math + .abs(evt.getX() - lastMousePress.getX())) { /* * on drag up or down, decrement or increment font size @@ -1042,7 +1377,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (newWidth > 0) { - ap.paintAlignment(false); + ap.paintAlignment(false, false); if (copyChanges) { /* @@ -1069,23 +1404,23 @@ public class SeqPanel extends JPanel implements MouseListener, if (!editingSeqs) { - doMouseDraggedDefineMode(evt); + dragStretchGroup(evt); return; } - int res = findColumn(evt); + int res = pos.column; if (res < 0) { res = 0; } - if ((lastres == -1) || (lastres == res)) + if ((editLastRes == -1) || (editLastRes == res)) { return; } - if ((res < av.getAlignment().getWidth()) && (res < lastres)) + if ((res < av.getAlignment().getWidth()) && (res < editLastRes)) { // dragLeft, delete gap editSequence(false, false, res); @@ -1098,20 +1433,44 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragging = true; if (scrollThread != null) { - scrollThread.setEvent(evt); + scrollThread.setMousePosition(evt.getPoint()); } } - // TODO: Make it more clever than many booleans + /** + * Edits the sequence to insert or delete one or more gaps, in response to a + * mouse drag or cursor mode command. The number of inserts/deletes may be + * specified with the cursor command, or else depends on the mouse event + * (normally one column, but potentially more for a fast mouse drag). + *
+ * Delete gaps is limited to the number of gaps left of the cursor position + * (mouse drag), or at or right of the cursor position (cursor mode). + *
+ * In group editing mode (Ctrl or Cmd down), the edit acts on all sequences in + * the current selection group. + *
+ * In locked editing mode (with a selection group present), inserts/deletions
+ * within the selection group are limited to its boundaries (and edits outside
+ * the group stop at its border).
+ *
+ * @param insertGap
+ * true to insert gaps, false to delete gaps
+ * @param editSeq
+ * (unused parameter)
+ * @param startres
+ * the column at which to perform the action; the number of columns
+ * affected depends on this.editLastRes
(cursor column
+ * position)
+ */
synchronized void editSequence(boolean insertGap, boolean editSeq,
- int startres)
+ final int startres)
{
int fixedLeft = -1;
int fixedRight = -1;
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.getAlignment().getSequenceAt(startseq);
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
// No group, but the sequence may represent a group
if (!groupEditing && av.hasHiddenRows())
@@ -1123,29 +1482,38 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
- StringBuilder message = new StringBuilder(64);
+ StringBuilder message = new StringBuilder(64); // for status bar
+
+ /*
+ * make a name for the edit action, for
+ * status bar message and Undo/Redo menu
+ */
+ String label = null;
if (groupEditing)
{
- message.append("Edit group:");
- if (editCommand == null)
- {
- editCommand = new EditCommand(
- MessageManager.getString("action.edit_group"));
- }
+ message.append("Edit group:");
+ label = MessageManager.getString("action.edit_group");
}
else
{
- message.append("Edit sequence: " + seq.getName());
- String label = seq.getName();
+ message.append("Edit sequence: " + seq.getName());
+ label = seq.getName();
if (label.length() > 10)
{
label = label.substring(0, 10);
}
- if (editCommand == null)
- {
- editCommand = new EditCommand(MessageManager.formatMessage(
- "label.edit_params", new String[] { label }));
- }
+ label = MessageManager.formatMessage("label.edit_params",
+ new String[]
+ { label });
+ }
+
+ /*
+ * initialise the edit command if there is not
+ * already one being extended
+ */
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand(label);
}
if (insertGap)
@@ -1157,13 +1525,17 @@ public class SeqPanel extends JPanel implements MouseListener,
message.append(" delete ");
}
- message.append(Math.abs(startres - lastres) + " gaps.");
- ap.alignFrame.statusBar.setText(message.toString());
+ message.append(Math.abs(startres - editLastRes) + " gaps.");
+ ap.alignFrame.setStatus(message.toString());
- // Are we editing within a selection group?
- if (groupEditing
- || (sg != null && sg.getSequences(av.getHiddenRepSequences())
- .contains(seq)))
+ /*
+ * is there a selection group containing the sequence being edited?
+ * if so the boundary of the group is the limit of the edit
+ * (but the edit may be inside or outside the selection group)
+ */
+ boolean inSelectionGroup = sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq);
+ if (groupEditing || inSelectionGroup)
{
fixedColumns = true;
@@ -1182,10 +1554,10 @@ public class SeqPanel extends JPanel implements MouseListener,
fixedLeft = sg.getStartRes();
fixedRight = sg.getEndRes();
- if ((startres < fixedLeft && lastres >= fixedLeft)
- || (startres >= fixedLeft && lastres < fixedLeft)
- || (startres > fixedRight && lastres <= fixedRight)
- || (startres <= fixedRight && lastres > fixedRight))
+ if ((startres < fixedLeft && editLastRes >= fixedLeft)
+ || (startres >= fixedLeft && editLastRes < fixedLeft)
+ || (startres > fixedRight && editLastRes <= fixedRight)
+ || (startres <= fixedRight && editLastRes > fixedRight))
{
endEditing();
return;
@@ -1207,12 +1579,12 @@ public class SeqPanel extends JPanel implements MouseListener,
{
fixedColumns = true;
int y1 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryLeft(startres);
+ .getNextHiddenBoundary(true, startres);
int y2 = av.getAlignment().getHiddenColumns()
- .getHiddenBoundaryRight(startres);
+ .getNextHiddenBoundary(false, startres);
- if ((insertGap && startres > y1 && lastres < y1)
- || (!insertGap && startres < y2 && lastres > y2))
+ if ((insertGap && startres > y1 && editLastRes < y1)
+ || (!insertGap && startres < y2 && editLastRes > y2))
{
endEditing();
return;
@@ -1233,6 +1605,54 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
+ boolean success = doEditSequence(insertGap, editSeq, startres,
+ fixedRight, fixedColumns, sg);
+
+ /*
+ * report what actually happened (might be less than
+ * what was requested), by inspecting the edit commands added
+ */
+ String msg = getEditStatusMessage(editCommand);
+ ap.alignFrame.setStatus(msg == null ? " " : msg);
+ if (!success)
+ {
+ endEditing();
+ }
+
+ editLastRes = startres;
+ seqCanvas.repaint();
+ }
+
+ /**
+ * A helper method that performs the requested editing to insert or delete
+ * gaps (if possible). Answers true if the edit was successful, false if could
+ * only be performed in part or not at all. Failure may occur in 'locked edit'
+ * mode, when an insertion requires a matching gapped position (or column) to
+ * delete, and deletion requires an adjacent gapped position (or column) to
+ * remove.
+ *
+ * @param insertGap
+ * true if inserting gap(s), false if deleting
+ * @param editSeq
+ * (unused parameter, currently always false)
+ * @param startres
+ * the column at which to perform the edit
+ * @param fixedRight
+ * fixed right boundary column of a locked edit (within or to the
+ * left of a selection group)
+ * @param fixedColumns
+ * true if this is a locked edit
+ * @param sg
+ * the sequence group (if group edit is being performed)
+ * @return
+ */
+ protected boolean doEditSequence(final boolean insertGap,
+ final boolean editSeq, final int startres, int fixedRight,
+ final boolean fixedColumns, final SequenceGroup sg)
+ {
+ final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
+ SequenceI[] seqs = new SequenceI[] { seq };
+
if (groupEditing)
{
List