X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1176df5583060aca696178a2dbdf6e45b0ac6f39;hb=87e1ada6a62777b415f14b0444fdcc63336c8f73;hp=3f740a1f36e82f23f7ba146f902c56edaa9b7305;hpb=620da661f54acba8fdb13f388dbed8b77d9113ed;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 3f740a1..1176df5 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -49,6 +49,7 @@ import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Color; @@ -164,9 +165,9 @@ public class SeqPanel extends JPanel */ private MousePos lastMousePosition; - protected int lastres; + protected int editLastRes; - protected int startseq; + protected int editStartSeq; protected AlignViewport av; @@ -255,7 +256,7 @@ public class SeqPanel extends JPanel int wrappedBlock = -1; /** - * Computes the column and sequence row (or possibly annotation row when in + * Computes the column and sequence row (and possibly annotation row when in * wrapped mode) for the given mouse position * * @param evt @@ -264,7 +265,7 @@ public class SeqPanel extends JPanel MousePos findMousePosition(MouseEvent evt) { int col = findColumn(evt); - int seq = -1; + int seqIndex = -1; int annIndex = -1; int y = evt.getY(); @@ -272,47 +273,52 @@ public class SeqPanel extends JPanel int alignmentHeight = av.getAlignment().getHeight(); if (av.getWrapAlignment()) { - int hgap = charHeight; - if (av.getScaleAboveWrapped()) - { - hgap += charHeight; - } + seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(), + seqCanvas.getHeight()); - final int alignmentHeightPixels = alignmentHeight * charHeight + hgap; - final int annotationHeight = seqCanvas.getAnnotationHeight(); - final int cHeight = alignmentHeightPixels + annotationHeight; + /* + * yPos modulo height of repeating width + */ + int yOffsetPx = y % seqCanvas.wrappedRepeatHeightPx; - int yOffsetPx = y % cHeight; // yPos below repeating width(s) - if (yOffsetPx > alignmentHeightPixels) + /* + * 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 + * 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); - // also last sequence in alignment (for backwards compatible behaviour) - seq = alignmentHeight - 1; + seqIndex = alignmentHeight - 1; } else { /* * mouse is over sequence (or the space above sequences) */ - yOffsetPx -= hgap; - if (yOffsetPx > 0) + yOffsetPx -= seqCanvas.wrappedSpaceAboveAlignment; + if (yOffsetPx >= 0) { - seq = Math.min(yOffsetPx / charHeight, alignmentHeight - 1); + seqIndex = Math.min(yOffsetPx / charHeight, alignmentHeight - 1); } } } else { - seq = Math.min((y / charHeight) + av.getRanges().getStartSeq(), + ViewportRanges ranges = av.getRanges(); + seqIndex = Math.min((y / charHeight) + ranges.getStartSeq(), alignmentHeight - 1); + seqIndex = Math.min(seqIndex, ranges.getEndSeq()); } - int seqIndex = seq; return new MousePos(col, seqIndex, annIndex); } @@ -328,10 +334,11 @@ public class SeqPanel extends JPanel 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()) { @@ -343,20 +350,30 @@ public class SeqPanel extends JPanel int y = evt.getY(); y = Math.max(0, y - hgap); - x = Math.max(0, x - seqCanvas.getLabelWidthWest()); + 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 + startOffset - + +Math.min(cwidth - 1, x / av.getCharWidth()); + + Math.min(cwidth - 1, x / charWidth); } else { @@ -365,7 +382,7 @@ public class SeqPanel extends JPanel * rather than right-hand gutter */ x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth()); - res = (x / av.getCharWidth()) + startRes; + res = (x / charWidth) + startRes; res = Math.min(res, av.getRanges().getEndRes()); } @@ -397,8 +414,8 @@ public class SeqPanel extends JPanel /* * Tidy up come what may... */ - startseq = -1; - lastres = -1; + editStartSeq = -1; + editLastRes = -1; editingSeqs = false; groupEditing = false; keyboardNo1 = null; @@ -626,8 +643,8 @@ public class SeqPanel extends JPanel 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(); } @@ -635,8 +652,8 @@ public class SeqPanel extends JPanel 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(); } @@ -645,8 +662,8 @@ public class SeqPanel extends JPanel { // 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(); } @@ -712,9 +729,8 @@ public class SeqPanel extends JPanel public void mouseReleased(MouseEvent evt) { MousePos pos = findMousePosition(evt); - if (pos.annotationIndex != -1) + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) { - // mouse is over annotation row in wrapped mode return; } @@ -729,13 +745,14 @@ public class SeqPanel extends JPanel return; } - if (!editingSeqs) + if (editingSeqs) + { + endEditing(); + } + else { doMouseReleasedDefineMode(evt, didDrag); - return; } - - endEditing(); } /** @@ -749,9 +766,8 @@ public class SeqPanel extends JPanel { lastMousePress = evt.getPoint(); MousePos pos = findMousePosition(evt); - if (pos.annotationIndex != -1) + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) { - // mouse is over an annotation row in wrapped mode return; } @@ -779,21 +795,16 @@ public class SeqPanel extends JPanel int seq = pos.seqIndex; int res = pos.column; - if (seq < 0 || res < 0) - { - return; - } - 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; @@ -838,7 +849,7 @@ public class SeqPanel extends JPanel // over residue to change abruptly, causing highlighted residue in panel 2 // to change, causing a scroll in panel 1 etc) ap.setToScrollComplementPanel(false); - wasScrolled = ap.scrollToPosition(results, false); + wasScrolled = ap.scrollToPosition(results); if (wasScrolled) { seqCanvas.revalidate(); @@ -906,7 +917,8 @@ public class SeqPanel extends JPanel { lastMousePosition = null; setToolTipText(null); - ap.alignFrame.statusBar.setText(""); + lastTooltip = null; + ap.alignFrame.setStatus(""); return; } @@ -998,7 +1010,8 @@ public class SeqPanel extends JPanel final int column = pos.column; final int rowIndex = pos.annotationIndex; - if (!av.getWrapAlignment() || !av.isShowAnnotation() || rowIndex < 0) + if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation() + || rowIndex < 0) { return; } @@ -1011,7 +1024,7 @@ public class SeqPanel extends JPanel String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column, anns[rowIndex]); - ap.alignFrame.statusBar.setText(msg); + ap.alignFrame.setStatus(msg); } private Point lastp = null; @@ -1024,20 +1037,26 @@ public class SeqPanel extends JPanel @Override public Point getToolTipLocation(MouseEvent event) { - int x = event.getX(), w = getWidth(); - int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too - // close to edge + if (tooltipText == null || tooltipText.length() <= 6) + { + lastp = null; + return null; + } + + int x = event.getX(); + int w = getWidth(); + // switch sides when tooltip is too close to edge + int wdth = (w - x < 200) ? -(w / 2) : 5; Point p = lastp; if (!event.isShiftDown() || p == null) { - p = (tooltipText != null && tooltipText.length() > 6) - ? new Point(event.getX() + wdth, event.getY() - 20) - : null; + p = new Point(event.getX() + wdth, event.getY() - 20); + lastp = p; } /* - * TODO: try to modify position region is not obcured by tooltip + * TODO: try to set position so region is not obscured by tooltip */ - return lastp = p; + return p; } String lastTooltip; @@ -1140,7 +1159,7 @@ public class SeqPanel extends JPanel text.append(" (").append(Integer.toString(residuePos)).append(")"); } - ap.alignFrame.statusBar.setText(text.toString()); + ap.alignFrame.setStatus(text.toString()); } /** @@ -1183,9 +1202,8 @@ public class SeqPanel extends JPanel public void mouseDragged(MouseEvent evt) { MousePos pos = findMousePosition(evt); - if (pos.isOverAnnotation()) + if (pos.isOverAnnotation() || pos.column == -1) { - // mouse is over annotation row in wrapped mode return; } @@ -1284,7 +1302,7 @@ public class SeqPanel extends JPanel if (!editingSeqs) { - doMouseDraggedDefineMode(evt); + dragStretchGroup(evt); return; } @@ -1295,12 +1313,12 @@ public class SeqPanel extends JPanel 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); @@ -1311,22 +1329,46 @@ public class SeqPanel extends JPanel } mouseDragging = true; - if ((scrollThread != null) && (scrollThread.isRunning())) + 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()) @@ -1338,30 +1380,38 @@ public class SeqPanel extends JPanel } } - 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) @@ -1373,12 +1423,17 @@ public class SeqPanel extends JPanel 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; @@ -1397,10 +1452,10 @@ public class SeqPanel extends JPanel 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; @@ -1426,8 +1481,8 @@ public class SeqPanel extends JPanel int y2 = av.getAlignment().getHiddenColumns() .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; @@ -1448,6 +1503,54 @@ public class SeqPanel extends JPanel } } + 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 vseqs = sg.getSequences(av.getHiddenRepSequences()); @@ -1466,7 +1569,8 @@ public class SeqPanel extends JPanel if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight && sg.getEndRes() == av.getAlignment().getWidth() - 1) { - sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); + sg.setEndRes( + av.getAlignment().getWidth() + startres - editLastRes); fixedRight = sg.getEndRes(); } @@ -1474,15 +1578,16 @@ public class SeqPanel extends JPanel // Find the next gap before the end // of the visible region boundary boolean blank = false; - for (; fixedRight > lastres; fixedRight--) + for (; fixedRight > editLastRes; fixedRight--) { blank = true; for (g = 0; g < groupSize; g++) { - for (int j = 0; j < startres - lastres; j++) + for (int j = 0; j < startres - editLastRes; j++) { - if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) + if (!Comparison + .isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -1499,12 +1604,11 @@ public class SeqPanel extends JPanel { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av.getAlignment() - .getHiddenColumns() - .getNextHiddenBoundary(false, startres))) + if ((av.hasHiddenColumns() + && startres < av.getAlignment().getHiddenColumns() + .getNextHiddenBoundary(false, startres))) { - endEditing(); - return; + return false; } int alWidth = av.getAlignment().getWidth(); @@ -1519,13 +1623,12 @@ public class SeqPanel extends JPanel } // We can still insert gaps if the selectionGroup // contains all the sequences - sg.setEndRes(sg.getEndRes() + startres - lastres); - fixedRight = alWidth + startres - lastres; + sg.setEndRes(sg.getEndRes() + startres - editLastRes); + fixedRight = alWidth + startres - editLastRes; } else { - endEditing(); - return; + return false; } } } @@ -1538,7 +1641,7 @@ public class SeqPanel extends JPanel for (g = 0; g < groupSize; g++) { - for (int j = startres; j < lastres; j++) + for (int j = startres; j < editLastRes; j++) { if (groupSeqs[g].getLength() <= j) { @@ -1548,8 +1651,7 @@ public class SeqPanel extends JPanel if (!Comparison.isGap(groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid - endEditing(); - return; + return false; } } } @@ -1560,15 +1662,15 @@ public class SeqPanel extends JPanel // dragging to the right if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, groupSeqs, fixedRight); + insertGap(j, groupSeqs, fixedRight); } } else { appendEdit(Action.INSERT_GAP, groupSeqs, startres, - startres - lastres); + startres - editLastRes, false); } } else @@ -1576,7 +1678,7 @@ public class SeqPanel extends JPanel // dragging to the left if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j > startres; j--) + for (int j = editLastRes; j > startres; j--) { deleteChar(startres, groupSeqs, fixedRight); } @@ -1584,28 +1686,36 @@ public class SeqPanel extends JPanel else { appendEdit(Action.DELETE_GAP, groupSeqs, startres, - lastres - startres); + editLastRes - startres, false); } - } } else - // ///Editing a single sequence/////////// { + /* + * editing a single sequence + */ if (insertGap) { // dragging to the right if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, new SequenceI[] { seq }, fixedRight); + if (!insertGap(j, seqs, fixedRight)) + { + /* + * e.g. cursor mode command specified + * more inserts than are possible + */ + return false; + } } } else { - appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, - startres - lastres); + appendEdit(Action.INSERT_GAP, seqs, editLastRes, + startres - editLastRes, false); } } else @@ -1615,21 +1725,20 @@ public class SeqPanel extends JPanel // dragging to the left if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j > startres; j--) + for (int j = editLastRes; j > startres; j--) { if (!Comparison.isGap(seq.getCharAt(startres))) { - endEditing(); - break; + return false; } - deleteChar(startres, new SequenceI[] { seq }, fixedRight); + deleteChar(startres, seqs, fixedRight); } } else { // could be a keyboard edit trying to delete none gaps int max = 0; - for (int m = startres; m < lastres; m++) + for (int m = startres; m < editLastRes; m++) { if (!Comparison.isGap(seq.getCharAt(m))) { @@ -1637,11 +1746,9 @@ public class SeqPanel extends JPanel } max++; } - if (max > 0) { - appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, - startres, max); + appendEdit(Action.DELETE_GAP, seqs, startres, max, false); } } } @@ -1649,25 +1756,82 @@ public class SeqPanel extends JPanel {// insertGap==false AND editSeq==TRUE; if (fixedColumns && fixedRight != -1) { - for (int j = lastres; j < startres; j++) + for (int j = editLastRes; j < startres; j++) { - insertChar(j, new SequenceI[] { seq }, fixedRight); + insertGap(j, seqs, fixedRight); } } else { - appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, - startres - lastres); + appendEdit(Action.INSERT_NUC, seqs, editLastRes, + startres - editLastRes, false); } } } } - lastres = startres; - seqCanvas.repaint(); + return true; + } + + /** + * Constructs an informative status bar message while dragging to insert or + * delete gaps. Answers null if inserts and deletes cancel out. + * + * @param editCommand + * a command containing the list of individual edits + * @return + */ + protected static String getEditStatusMessage(EditCommand editCommand) + { + if (editCommand == null) + { + return null; + } + + /* + * add any inserts, and subtract any deletes, + * not counting those auto-inserted when doing a 'locked edit' + * (so only counting edits 'under the cursor') + */ + int count = 0; + for (Edit cmd : editCommand.getEdits()) + { + if (!cmd.isSystemGenerated()) + { + count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber() + : -cmd.getNumber(); + } + } + + if (count == 0) + { + /* + * inserts and deletes cancel out + */ + return null; + } + + String msgKey = count > 1 ? "label.insert_gaps" + : (count == 1 ? "label.insert_gap" + : (count == -1 ? "label.delete_gap" + : "label.delete_gaps")); + count = Math.abs(count); + + return MessageManager.formatMessage(msgKey, String.valueOf(count)); } - void insertChar(int j, SequenceI[] seq, int fixedColumn) + /** + * Inserts one gap at column j, deleting the right-most gapped column up to + * (and including) fixedColumn. Returns true if the edit is successful, false + * if no blank column is available to allow the insertion to be balanced by a + * deletion. + * + * @param j + * @param seq + * @param fixedColumn + * @return + */ + boolean insertGap(int j, SequenceI[] seq, int fixedColumn) { int blankColumn = fixedColumn; for (int s = 0; s < seq.length; s++) @@ -1688,47 +1852,60 @@ public class SeqPanel extends JPanel { blankColumn = fixedColumn; endEditing(); - return; + return false; } } - appendEdit(Action.DELETE_GAP, seq, blankColumn, 1); + appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, true); - appendEdit(Action.INSERT_GAP, seq, j, 1); + appendEdit(Action.INSERT_GAP, seq, j, 1, false); + return true; } /** - * Helper method to add and perform one edit action. + * Helper method to add and perform one edit action * * @param action * @param seq * @param pos * @param count + * @param systemGenerated + * true if the edit is a 'balancing' delete (or insert) to match a + * user's insert (or delete) in a locked editing region */ protected void appendEdit(Action action, SequenceI[] seq, int pos, - int count) + int count, boolean systemGenerated) { final Edit edit = new EditCommand().new Edit(action, seq, pos, count, av.getAlignment().getGapCharacter()); + edit.setSystemGenerated(systemGenerated); editCommand.appendEdit(edit, av.getAlignment(), true, null); } - void deleteChar(int j, SequenceI[] seq, int fixedColumn) + /** + * Deletes the character at column j, and inserts a gap at fixedColumn, in + * each of the given sequences. The caller should ensure that all sequences + * are gapped in column j. + * + * @param j + * @param seqs + * @param fixedColumn + */ + void deleteChar(int j, SequenceI[] seqs, int fixedColumn) { + appendEdit(Action.DELETE_GAP, seqs, j, 1, false); - appendEdit(Action.DELETE_GAP, seq, j, 1); - - appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1); + appendEdit(Action.INSERT_GAP, seqs, fixedColumn, 1, true); } /** - * DOCUMENT ME! + * On reentering the panel, stops any scrolling that was started on dragging + * out of the panel * * @param e - * DOCUMENT ME! */ @Override public void mouseEntered(MouseEvent e) @@ -1737,23 +1914,20 @@ public class SeqPanel extends JPanel { oldSeq = 0; } - - if ((scrollThread != null) && (scrollThread.isRunning())) - { - scrollThread.stopScrolling(); - scrollThread = null; - } + stopScrolling(); } /** - * DOCUMENT ME! + * On leaving the panel, if the mouse is being dragged, starts a thread to + * scroll it until the mouse is released (in unwrapped mode only) * * @param e - * DOCUMENT ME! */ @Override public void mouseExited(MouseEvent e) { + lastMousePosition = null; + ap.alignFrame.setStatus(" "); if (av.getWrapAlignment()) { return; @@ -1775,9 +1949,8 @@ public class SeqPanel extends JPanel { SequenceGroup sg = null; MousePos pos = findMousePosition(evt); - if (pos.isOverAnnotation()) + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) { - // mouse is over annotation label in wrapped mode return; } @@ -1796,7 +1969,7 @@ public class SeqPanel extends JPanel * find features at the position (if not gapped), or straddling * the position (if at a gap) */ - SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex);// findSeq(evt)); + SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex); List features = seqCanvas.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); @@ -1868,13 +2041,8 @@ public class SeqPanel extends JPanel */ protected void doMousePressedDefineMode(MouseEvent evt, MousePos pos) { - if (pos.isOverAnnotation()) + if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1) { - // JvOptionPane.showInternalMessageDialog(Desktop.desktop, - // MessageManager.getString( - // "label.cannot_edit_annotations_in_wrapped_view"), - // MessageManager.getString("label.wrapped_view_no_edit"), - // JvOptionPane.WARNING_MESSAGE); return; } @@ -1885,11 +2053,6 @@ public class SeqPanel extends JPanel startWrapBlock = wrappedBlock; - if (seq < 0 || res < 0) - { - return; - } - SequenceI sequence = av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) @@ -2012,7 +2175,8 @@ public class SeqPanel extends JPanel * true if this event is happening after a mouse drag (rather than a * mouse down) */ - public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag) + protected void doMouseReleasedDefineMode(MouseEvent evt, + boolean afterDrag) { if (stretchGroup == null) { @@ -2028,8 +2192,11 @@ public class SeqPanel extends JPanel && afterDrag; if (stretchGroup.cs != null) { - stretchGroup.cs.alignmentChanged(stretchGroup, - av.getHiddenRepSequences()); + if (afterDrag) + { + stretchGroup.cs.alignmentChanged(stretchGroup, + av.getHiddenRepSequences()); + } ResidueShaderI groupColourScheme = stretchGroup .getGroupColourScheme(); @@ -2055,17 +2222,21 @@ public class SeqPanel extends JPanel } /** - * DOCUMENT ME! + * Resizes the borders of a selection group depending on the direction of + * mouse drag * * @param evt - * DOCUMENT ME! */ - public void doMouseDraggedDefineMode(MouseEvent evt) + protected void dragStretchGroup(MouseEvent evt) { + if (stretchGroup == null) + { + return; + } + MousePos pos = findMousePosition(evt); - if (pos.isOverAnnotation()) + if (pos.isOverAnnotation() || pos.column == -1 || pos.seqIndex == -1) { - // mouse is over annotation in wrapped mode return; } @@ -2077,15 +2248,7 @@ public class SeqPanel extends JPanel return; } - if (stretchGroup == null) - { - return; - } - - if (res >= av.getAlignment().getWidth()) - { - res = av.getAlignment().getWidth() - 1; - } + res = Math.min(res, av.getAlignment().getWidth()-1); if (stretchGroup.getEndRes() == res) { @@ -2171,89 +2334,152 @@ public class SeqPanel extends JPanel mouseDragging = true; - if ((scrollThread != null) && (scrollThread.isRunning())) + if (scrollThread != null) { - scrollThread.setEvent(evt); + scrollThread.setMousePosition(evt.getPoint()); } + + /* + * construct a status message showing the range of the selection + */ + StringBuilder status = new StringBuilder(64); + List seqs = stretchGroup.getSequences(); + String name = seqs.get(0).getName(); + if (name.length() > 20) + { + name = name.substring(0, 20); + } + status.append(name).append(" - "); + name = seqs.get(seqs.size() - 1).getName(); + if (name.length() > 20) + { + name = name.substring(0, 20); + } + status.append(name).append(" "); + int startRes = stretchGroup.getStartRes(); + status.append(" cols ").append(String.valueOf(startRes + 1)) + .append("-"); + int endRes = stretchGroup.getEndRes(); + status.append(String.valueOf(endRes + 1)); + status.append(" (").append(String.valueOf(seqs.size())).append(" x ") + .append(String.valueOf(endRes - startRes + 1)).append(")"); + ap.alignFrame.setStatus(status.toString()); } - void scrollCanvas(MouseEvent evt) + /** + * Stops the scroll thread if it is running + */ + void stopScrolling() { - if (evt == null) + if (scrollThread != null) { - if ((scrollThread != null) && (scrollThread.isRunning())) - { - scrollThread.stopScrolling(); - scrollThread = null; - } - mouseDragging = false; + scrollThread.stopScrolling(); + scrollThread = null; } - else - { - if (scrollThread == null) - { - scrollThread = new ScrollThread(); - } + mouseDragging = false; + } - mouseDragging = true; - scrollThread.setEvent(evt); + /** + * Starts a thread to scroll the alignment, towards a given mouse position + * outside the panel bounds + * + * @param mousePos + */ + void startScrolling(Point mousePos) + { + if (scrollThread == null) + { + scrollThread = new ScrollThread(); } + mouseDragging = true; + scrollThread.setMousePosition(mousePos); } - // this class allows scrolling off the bottom of the visible alignment + /** + * Performs scrolling of the visible alignment left, right, up or down + */ class ScrollThread extends Thread { - MouseEvent evt; + private Point mousePos; private volatile boolean threadRunning = true; + /** + * Constructor + */ public ScrollThread() { + setName("SeqPanel$ScrollThread"); start(); } - public void setEvent(MouseEvent e) + /** + * Sets the position of the mouse that determines the direction of the + * scroll to perform + * + * @param p + */ + public void setMousePosition(Point p) { - evt = e; + mousePos = p; } + /** + * Sets a flag that will cause the thread to exit + */ public void stopScrolling() { threadRunning = false; } - public boolean isRunning() - { - return threadRunning; - } - + /** + * Scrolls the alignment left or right, and/or up or down, depending on the + * last notified mouse position, until the limit of the alignment is + * reached, or a flag is set to stop the scroll + */ @Override public void run() { - while (threadRunning) + while (threadRunning && mouseDragging) { - if (evt != null) + if (mousePos != null) { - if (mouseDragging && (evt.getY() < 0) - && (av.getRanges().getStartSeq() > 0)) + boolean scrolled = false; + ViewportRanges ranges = SeqPanel.this.av.getRanges(); + + /* + * scroll up or down + */ + if (mousePos.y < 0) { - av.getRanges().scrollUp(true); + // mouse is above this panel - try scroll up + scrolled = ranges.scrollUp(true); } - - if (mouseDragging && (evt.getY() >= getHeight()) && (av - .getAlignment().getHeight() > av.getRanges().getEndSeq())) + else if (mousePos.y >= getHeight()) { - av.getRanges().scrollUp(false); + // mouse is below this panel - try scroll down + scrolled = ranges.scrollUp(false); } - if (mouseDragging && (evt.getX() < 0)) + /* + * scroll left or right + */ + if (mousePos.x < 0) { - av.getRanges().scrollRight(false); + scrolled |= ranges.scrollRight(false); } - else if (mouseDragging && (evt.getX() >= getWidth())) + else if (mousePos.x >= getWidth()) { - av.getRanges().scrollRight(true); + scrolled |= ranges.scrollRight(true); + } + if (!scrolled) + { + /* + * we have reached the limit of the visible alignment - quit + */ + threadRunning = false; + SeqPanel.this.ap.repaint(); } } @@ -2443,7 +2669,7 @@ public class SeqPanel extends JPanel HiddenColumns hs = new HiddenColumns(); MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs); av.setColumnSelection(cs); - av.getAlignment().setHiddenColumns(hs); + boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs); // lastly, update any dependent dialogs if (ap.getCalculationDialog() != null) @@ -2451,7 +2677,11 @@ public class SeqPanel extends JPanel ap.getCalculationDialog().validateCalcTypes(); } - PaintRefresher.Refresh(this, av.getSequenceSetId()); + /* + * repaint alignment, and also Overview or Structure + * if hidden column selection has changed + */ + ap.paintAlignment(hiddenChanged, hiddenChanged); return true; }