X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=71e9f4eb9c9e3556524ff2476bdb1cdfbd51d280;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=f121d1158100d76f4ff2abdbf47fc5fe1f8decc1;hpb=4be681e59be335eecdee2bfea9d59856d7cb8f70;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index f121d11..71e9f4e 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,19 +1,20 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; @@ -146,7 +147,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( seqCanvas.cursorY); - seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1); + seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; scrollToVisible(); } @@ -154,7 +155,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; - if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() + && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; int maxWidth = av.getAlignment().getWidth(); @@ -287,7 +289,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, else { // Now add any sequences between min and max - sg.getSequences(null).removeAllElements(); + sg.clear(); for (int i = min; i < max; i++) { sg.addSequence(av.getAlignment().getSequenceAt(i), false); @@ -341,31 +343,35 @@ public class SeqPanel extends Panel implements MouseMotionListener, keyboardNo1.append(value); } } - int getKeyboardNo1() { - if (keyboardNo1 == null) - return 1; - else + try { + if (keyboardNo1 != null) { int value = Integer.parseInt(keyboardNo1.toString()); keyboardNo1 = null; return value; } + } catch (Exception x) + {} + keyboardNo1 = null; + return 1; } int getKeyboardNo2() { - if (keyboardNo2 == null) - return 1; - else - { + try { + if (keyboardNo2!=null){ int value = Integer.parseInt(keyboardNo2.toString()); keyboardNo2 = null; return value; } + } catch (Exception x) + {} + keyboardNo2 = null; + return 1; } - + void setStatusMessage(SequenceI sequence, int res, int seq) { StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " @@ -458,7 +464,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); if (evt.getClickCount() > 1) { - if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() == 1 + if (av.getSelectionGroup() != null + && av.getSelectionGroup().getSize() == 1 && av.getSelectionGroup().getEndRes() - av.getSelectionGroup().getStartRes() < 2) { @@ -581,8 +588,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), - av.getAlignment().getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment() + .getHeight() - 1); if (seq < 0) { seq = -1; @@ -590,8 +597,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, } else { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), - av.getAlignment().getHeight() - 1); + seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + .getAlignment().getHeight() - 1); if (seq < 0) { seq = -1; @@ -1036,13 +1043,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (groupEditing) { - Vector vseqs = sg.getSequences(av.getHiddenRepSequences()); - int g, groupSize = vseqs.size(); - SequenceI[] groupSeqs = new SequenceI[groupSize]; - for (g = 0; g < groupSeqs.length; g++) - { - groupSeqs[g] = (SequenceI) vseqs.elementAt(g); - } + SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences()) + .toArray(new SequenceI[0]); // drag to right if (insertGap) @@ -1064,12 +1066,12 @@ public class SeqPanel extends Panel implements MouseMotionListener, { blank = true; - for (g = 0; g < groupSize; g++) + for (SequenceI gs : groupSeqs) { for (int j = 0; j < startres - lastres; j++) { - if (!jalview.util.Comparison.isGap(groupSeqs[g] - .getCharAt(fixedRight - j))) + if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight + - j))) { blank = false; break; @@ -1086,8 +1088,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, { if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns() && startres < av.getColumnSelection() - .getHiddenBoundaryRight(startres))) + if ((av.hasHiddenColumns() && startres < av + .getColumnSelection().getHiddenBoundaryRight(startres))) { endEditing(); return; @@ -1096,7 +1098,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, int alWidth = av.getAlignment().getWidth(); if (av.hasHiddenRows()) { - int hwidth = av.getAlignment().getHiddenSequences().getWidth(); + int hwidth = av.getAlignment().getHiddenSequences() + .getWidth(); if (hwidth > alWidth) { alWidth = hwidth; @@ -1121,16 +1124,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, // / Are we able to delete? // ie are all columns blank? - for (g = 0; g < groupSize; g++) + for (SequenceI gs : groupSeqs) { for (int j = startres; j < lastres; j++) { - if (groupSeqs[g].getLength() <= j) + if (gs.getLength() <= j) { continue; } - if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j))) + if (!jalview.util.Comparison.isGap(gs.getCharAt(j))) { // Not a gap, block edit not valid endEditing(); @@ -1264,16 +1267,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(), - true); + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, + av.getAlignment(), true); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(), - true); + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, + av.getAlignment(), true); editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, av.getAlignment(), true); @@ -1417,28 +1420,17 @@ public class SeqPanel extends Panel implements MouseMotionListener, return; } + stretchGroup.recalcConservation(); // always do this - annotation has own + // state if (stretchGroup.cs != null) { - if (stretchGroup.cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme) stretchGroup.cs).resetClustalX( - stretchGroup.getSequences(av.getHiddenRepSequences()), - stretchGroup.getWidth()); - } - - if (stretchGroup.cs instanceof Blosum62ColourScheme - || stretchGroup.cs instanceof PIDColourScheme - || stretchGroup.cs.conservationApplied() - || stretchGroup.cs.getThreshold() > 0) - { - stretchGroup.recalcConservation(); - } + stretchGroup.cs.alignmentChanged(stretchGroup, + av.getHiddenRepSequences()); if (stretchGroup.cs.conservationApplied()) { SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); - stretchGroup.recalcConservation(); } else { @@ -1523,7 +1515,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, dragDirection = -1; } - while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().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. @@ -1710,7 +1703,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true)) { SequenceGroup sgroup = null; - if (seqsel != null && seqsel.getSize()>0) + if (seqsel != null && seqsel.getSize() > 0) { if (av.getAlignment() == null) { @@ -1740,7 +1733,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, } repaint = av.isSelectionGroupChanged(true); } - if (copycolsel && (av.getColumnSelection() == null || !av.isColSelChanged(true))) + if (copycolsel + && (av.getColumnSelection() == null || !av + .isColSelChanged(true))) { // the current selection is unset or from a previous message // so import the new colsel. @@ -1765,8 +1760,10 @@ public class SeqPanel extends Panel implements MouseMotionListener, } repaint |= av.isColSelChanged(true); } - if (copycolsel && av.hasHiddenColumns() - && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null)) + if (copycolsel + && av.hasHiddenColumns() + && (av.getColumnSelection() == null || av.getColumnSelection() + .getHiddenColumns() == null)) { System.err.println("Bad things"); } @@ -1779,35 +1776,40 @@ public class SeqPanel extends Panel implements MouseMotionListener, /** * scroll to the given row/column - or nearest visible location + * * @param row * @param column */ public void scrollTo(int row, int column) { - - row = row<0 ? ap.av.startSeq : row; - column = column<0 ? ap.av.startRes : column; - ap.scrollTo(row, row, column, true, true); + + row = row < 0 ? ap.av.startSeq : row; + column = column < 0 ? ap.av.startRes : column; + ap.scrollTo(column, column, row, true, true); } + /** * scroll to the given row - or nearest visible location + * * @param row */ public void scrollToRow(int row) { - - row = row<0 ? ap.av.startSeq : row; - ap.scrollTo(row, row, ap.av.startRes, true, true); + + row = row < 0 ? ap.av.startSeq : row; + ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true); } + /** * scroll to the given column - or nearest visible location + * * @param column */ public void scrollToColumn(int column) { - - column = column<0 ? ap.av.startRes : column; - ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true); + + column = column < 0 ? ap.av.startRes : column; + ap.scrollTo(column, column, ap.av.startSeq, true, true); } }