X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=f121d1158100d76f4ff2abdbf47fc5fe1f8decc1;hb=6bd9630607bd38aaf9b42738a0ae90de8fe5c6e8;hp=cce8c23b6d704af80cfb5894907f761a6eb07785;hpb=9e3e20c98eae9498a68bb0a770359564797a12ef;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index cce8c23..f121d11 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -154,19 +154,19 @@ public class SeqPanel extends Panel implements MouseMotionListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; - if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; - int maxWidth = av.alignment.getWidth(); + int maxWidth = av.getAlignment().getWidth(); - while (!av.colSel.isVisible(seqCanvas.cursorX) + while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.colSel.isVisible(seqCanvas.cursorX)) + || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@ -180,18 +180,18 @@ public class SeqPanel extends Panel implements MouseMotionListener, { seqCanvas.cursorX = 0; } - else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) + else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1) { - seqCanvas.cursorX = av.alignment.getWidth() - 1; + seqCanvas.cursorX = av.getAlignment().getWidth() - 1; } if (seqCanvas.cursorY < 0) { seqCanvas.cursorY = 0; } - else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1) { - seqCanvas.cursorY = av.alignment.getHeight() - 1; + seqCanvas.cursorY = av.getAlignment().getHeight() - 1; } endEditing(); @@ -209,7 +209,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { ap.scrollUp(false); } - while (seqCanvas.cursorX < av.colSel + while (seqCanvas.cursorX < av.getColumnSelection() .adjustForHiddenColumns(av.startRes)) { @@ -218,7 +218,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, break; } } - while (seqCanvas.cursorX > av.colSel + while (seqCanvas.cursorX > av.getColumnSelection() .adjustForHiddenColumns(av.endRes)) { if (!ap.scrollRight(true)) @@ -227,7 +227,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } } - setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); seqCanvas.repaint(); @@ -240,12 +240,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (av.getSelectionGroup() != null) { - SequenceGroup sg = av.selectionGroup; + SequenceGroup sg = av.getSelectionGroup(); // Find the top and bottom of this group - int min = av.alignment.getHeight(), max = 0; + int min = av.getAlignment().getHeight(), max = 0; for (int i = 0; i < sg.getSize(); i++) { - int index = av.alignment.findIndex(sg.getSequenceAt(i)); + int index = av.getAlignment().findIndex(sg.getSequenceAt(i)); if (index > max) { max = index; @@ -290,7 +290,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, sg.getSequences(null).removeAllElements(); for (int i = min; i < max; i++) { - sg.addSequence(av.alignment.getSequenceAt(i), false); + sg.addSequence(av.getAlignment().getSequenceAt(i), false); } } } @@ -372,7 +372,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, + sequence.getName()); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + ""); @@ -455,10 +455,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, public void mouseClicked(MouseEvent evt) { - SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt)); + SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); if (evt.getClickCount() > 1) { - if (av.getSelectionGroup().getSize() == 1 + if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() == 1 && av.getSelectionGroup().getEndRes() - av.getSelectionGroup().getStartRes() < 2) { @@ -543,7 +543,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, res = (x / av.getCharWidth()) + av.getStartRes(); } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } @@ -582,7 +582,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, y -= hgap; seq = Math.min((y % cHeight) / av.getCharHeight(), - av.alignment.getHeight() - 1); + av.getAlignment().getHeight() - 1); if (seq < 0) { seq = -1; @@ -591,7 +591,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, else { seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), - av.alignment.getHeight() - 1); + av.getAlignment().getHeight() - 1); if (seq < 0) { seq = -1; @@ -688,7 +688,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, + sequence.getName()); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + ""); @@ -717,7 +717,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, ap.alignFrame.statusBar.setText(text.toString()); StringBuffer tooltipText = new StringBuffer(); - SequenceGroup[] groups = av.alignment.findAllGroups(sequence); + SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) { for (int g = 0; g < groups.length; g++) @@ -916,14 +916,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); - SequenceI seq = av.alignment.getSequenceAt(startseq); + SequenceI seq = av.getAlignment().getSequenceAt(startseq); - if (!groupEditing && av.hasHiddenRows) + if (!groupEditing && av.hasHiddenRows()) { - if (av.hiddenRepSequences != null - && av.hiddenRepSequences.containsKey(seq)) + if (av.isHiddenRepSequence(seq)) { - sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + sg = (SequenceGroup) av.getRepresentedSequences(seq); groupEditing = true; } } @@ -965,7 +964,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, // Are we editing within a selection group? if (groupEditing - || (sg != null && sg.getSequences(av.hiddenRepSequences) + || (sg != null && sg.getSequences(av.getHiddenRepSequences()) .contains(seq))) { fixedColumns = true; @@ -974,14 +973,13 @@ public class SeqPanel extends Panel implements MouseMotionListener, // but the sequence represents a group if (sg == null) { - if (av.hiddenRepSequences == null - || !av.hiddenRepSequences.containsKey(seq)) + if (!av.isHiddenRepSequence(seq)) { endEditing(); return; } - sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + sg = av.getRepresentedSequences(seq); } fixedLeft = sg.getStartRes(); @@ -1008,7 +1006,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { fixedColumns = true; int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); @@ -1038,7 +1036,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (groupEditing) { - Vector vseqs = sg.getSequences(av.hiddenRepSequences); + Vector vseqs = sg.getSequences(av.getHiddenRepSequences()); int g, groupSize = vseqs.size(); SequenceI[] groupSeqs = new SequenceI[groupSize]; for (g = 0; g < groupSeqs.length; g++) @@ -1052,9 +1050,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, // If the user has selected the whole sequence, and is dragging to // the right, we can still extend the alignment and selectionGroup if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight - && sg.getEndRes() == av.alignment.getWidth() - 1) + && sg.getEndRes() == av.getAlignment().getWidth() - 1) { - sg.setEndRes(av.alignment.getWidth() + startres - lastres); + sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); fixedRight = sg.getEndRes(); } @@ -1086,19 +1084,19 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (!blank) { - if (sg.getSize() == av.alignment.getHeight()) + if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns && startres < av.getColumnSelection() + if ((av.hasHiddenColumns() && startres < av.getColumnSelection() .getHiddenBoundaryRight(startres))) { endEditing(); return; } - int alWidth = av.alignment.getWidth(); - if (av.hasHiddenRows) + int alWidth = av.getAlignment().getWidth(); + if (av.hasHiddenRows()) { - int hwidth = av.alignment.getHiddenSequences().getWidth(); + int hwidth = av.getAlignment().getHiddenSequences().getWidth(); if (hwidth > alWidth) { alWidth = hwidth; @@ -1155,7 +1153,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, else { editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.alignment, true); + startres, startres - lastres, av.getAlignment(), true); } } else @@ -1171,7 +1169,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, else { editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.alignment, true); + startres, lastres - startres, av.getAlignment(), true); } } @@ -1193,7 +1191,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, else { editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.alignment, true); + { seq }, lastres, startres - lastres, av.getAlignment(), true); } } else @@ -1228,7 +1226,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (max > 0) { editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] - { seq }, startres, max, av.alignment, true); + { seq }, startres, max, av.getAlignment(), true); } } } @@ -1264,9 +1262,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, } editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, - av.alignment, true); + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment, + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(), true); } @@ -1274,11 +1272,11 @@ public class SeqPanel extends Panel implements MouseMotionListener, void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment, + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(), true); editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, - av.alignment, true); + av.getAlignment(), true); } // //////////////////////////////////////// @@ -1313,7 +1311,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (stretchGroup == null) { - stretchGroup = av.alignment.findGroup(sequence); + stretchGroup = av.getAlignment().findGroup(sequence); if (stretchGroup != null && res > stretchGroup.getStartRes() && res < stretchGroup.getEndRes()) { @@ -1331,7 +1329,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { stretchGroup = null; - SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); if (allGroups != null) { @@ -1424,7 +1422,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (stretchGroup.cs instanceof ClustalxColourScheme) { ((ClustalxColourScheme) stretchGroup.cs).resetClustalX( - stretchGroup.getSequences(av.hiddenRepSequences), + stretchGroup.getSequences(av.getHiddenRepSequences()), stretchGroup.getWidth()); } @@ -1473,14 +1471,14 @@ public class SeqPanel extends Panel implements MouseMotionListener, mouseDragging = true; - if (y > av.alignment.getHeight()) + if (y > av.getAlignment().getHeight()) { - y = av.alignment.getHeight() - 1; + y = av.getAlignment().getHeight() - 1; } - if (res >= av.alignment.getWidth()) + if (res >= av.getAlignment().getWidth()) { - res = av.alignment.getWidth() - 1; + res = av.getAlignment().getWidth() - 1; } if (stretchGroup.getEndRes() == res) @@ -1525,7 +1523,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, dragDirection = -1; } - while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight())) { // This routine ensures we don't skip any sequences, as the // selection is quite slow. @@ -1662,7 +1660,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } if (mouseDragging && evt.getY() >= getSize().height - && av.alignment.getHeight() > av.getEndSeq()) + && av.getAlignment().getHeight() > av.getEndSeq()) { running = ap.scrollUp(false); } @@ -1709,12 +1707,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, // rules are: colsel is copied if there is a real intersection between // sequence selection boolean repaint = false, copycolsel = true; - if (av.selectionGroup == null || !av.isSelectionGroupChanged()) + if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true)) { SequenceGroup sgroup = null; if (seqsel != null && seqsel.getSize()>0) { - if (av.alignment == null) + if (av.getAlignment() == null) { System.out .println("Selection message: alignviewport av SeqSetId=" @@ -1723,8 +1721,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, + " 's alignment is NULL! returning immediatly."); return; } - sgroup = seqsel.intersect(av.alignment, - (av.hasHiddenRows) ? av.hiddenRepSequences : null); + sgroup = seqsel.intersect(av.getAlignment(), + (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); if ((sgroup == null || sgroup.getSize() == 0) && (colsel == null || colsel.size() == 0)) { @@ -1740,35 +1738,35 @@ public class SeqPanel extends Panel implements MouseMotionListener, { av.setSelectionGroup(null); } - repaint = av.isSelectionGroupChanged(); + repaint = av.isSelectionGroupChanged(true); } - if (copycolsel && (av.colSel == null || !av.isColSelChanged())) + if (copycolsel && (av.getColumnSelection() == null || !av.isColSelChanged(true))) { // the current selection is unset or from a previous message // so import the new colsel. if (colsel == null || colsel.size() == 0) { - if (av.colSel != null) + if (av.getColumnSelection() != null) { - av.colSel.clear(); + av.getColumnSelection().clear(); } } else { // TODO: shift colSel according to the intersecting sequences - if (av.colSel == null) + if (av.getColumnSelection() == null) { - av.colSel = new ColumnSelection(colsel); + av.setColumnSelection(new ColumnSelection(colsel)); } else { - av.colSel.setElementsFrom(colsel); + av.getColumnSelection().setElementsFrom(colsel); } } - repaint |= av.isColSelChanged(); + repaint |= av.isColSelChanged(true); } - if (copycolsel && av.hasHiddenColumns - && (av.colSel == null || av.colSel.getHiddenColumns() == null)) + if (copycolsel && av.hasHiddenColumns() + && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null)) { System.err.println("Bad things"); }