X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=e7d90300fc3af87550608b97a80679d5c883731f;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=ad5e052a17af0a4e9bf2d81cd27ec44039df45ca;hpb=53ec6ec5b4b6288bd8f33162a9974cc3a0a16c91;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index ad5e052..e7d9030 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,20 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.gui; @@ -62,7 +62,7 @@ public class SeqCanvas extends JComponent * Creates a new SeqCanvas object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public SeqCanvas(AlignmentPanel ap) { @@ -88,13 +88,13 @@ public class SeqCanvas extends JComponent * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param startx - * DOCUMENT ME! + * DOCUMENT ME! * @param endx - * DOCUMENT ME! + * DOCUMENT ME! * @param ypos - * DOCUMENT ME! + * DOCUMENT ME! */ void drawNorthScale(Graphics g, int startx, int endx, int ypos) { @@ -106,7 +106,7 @@ public class SeqCanvas extends JComponent for (int i = scalestartx; i < endx; i += 10) { int value = i; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { value = av.getColumnSelection().adjustForHiddenColumns(value); } @@ -125,35 +125,35 @@ public class SeqCanvas extends JComponent * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param startx - * DOCUMENT ME! + * DOCUMENT ME! * @param endx - * DOCUMENT ME! + * DOCUMENT ME! * @param ypos - * DOCUMENT ME! + * DOCUMENT ME! */ void drawWestScale(Graphics g, int startx, int endx, int ypos) { FontMetrics fm = getFontMetrics(av.getFont()); ypos += av.charHeight; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { startx = av.getColumnSelection().adjustForHiddenColumns(startx); endx = av.getColumnSelection().adjustForHiddenColumns(endx); } - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } // WEST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - SequenceI seq = av.alignment.getSequenceAt(i); + SequenceI seq = av.getAlignment().getSequenceAt(i); int index = startx; int value = -1; @@ -166,7 +166,7 @@ public class SeqCanvas extends JComponent continue; } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = av.getAlignment().getSequenceAt(i).findPosition(index); break; } @@ -185,28 +185,28 @@ public class SeqCanvas extends JComponent * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param startx - * DOCUMENT ME! + * DOCUMENT ME! * @param endx - * DOCUMENT ME! + * DOCUMENT ME! * @param ypos - * DOCUMENT ME! + * DOCUMENT ME! */ void drawEastScale(Graphics g, int startx, int endx, int ypos) { ypos += av.charHeight; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { endx = av.getColumnSelection().adjustForHiddenColumns(endx); } SequenceI seq; // EAST SCALE - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - seq = av.alignment.getSequenceAt(i); + seq = av.getAlignment().getSequenceAt(i); int index = endx; int value = -1; @@ -239,9 +239,9 @@ public class SeqCanvas extends JComponent * slider adjustment * * @param horizontal - * shift along + * shift along * @param vertical - * shift up or down in repaint + * shift up or down in repaint */ public void fastPaint(int horizontal, int vertical) { @@ -322,7 +322,7 @@ public class SeqCanvas extends JComponent public void paintComponent(Graphics g) { BufferedImage lcimg = img; // take reference since other threads may null - // img and call later. + // img and call later. super.paintComponent(g); if (lcimg != null @@ -392,7 +392,7 @@ public class SeqCanvas extends JComponent * DOCUMENT ME! * * @param cwidth - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -426,9 +426,9 @@ public class SeqCanvas extends JComponent String mask = "00"; int maxWidth = 0; int tmp; - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { - tmp = av.alignment.getSequenceAt(i).getEnd(); + tmp = av.getAlignment().getSequenceAt(i).getEnd(); if (tmp > maxWidth) { maxWidth = tmp; @@ -446,13 +446,13 @@ public class SeqCanvas extends JComponent * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param canvasWidth - * DOCUMENT ME! + * DOCUMENT ME! * @param canvasHeight - * DOCUMENT ME! + * DOCUMENT ME! * @param startRes - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) @@ -486,9 +486,9 @@ public class SeqCanvas extends JComponent int endx; int ypos = hgap; - int maxwidth = av.alignment.getWidth() - 1; + int maxwidth = av.getAlignment().getWidth() - 1; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -524,7 +524,7 @@ public class SeqCanvas extends JComponent drawNorthScale(g, startRes, endx, ypos); } - if (av.hasHiddenColumns && av.showHiddenMarkers) + if (av.hasHiddenColumns() && av.showHiddenMarkers) { g.setColor(Color.blue); int res; @@ -573,7 +573,8 @@ public class SeqCanvas extends JComponent annotations = new AnnotationPanel(av); } - annotations.drawComponent((Graphics2D) g, startRes, endx + 1); + annotations.renderer.drawComponent(annotations, av, (Graphics2D) g, + -1, startRes, endx + 1); g.translate(0, -cHeight - ypos - 3); } g.setClip(clip); @@ -606,22 +607,22 @@ public class SeqCanvas extends JComponent * DOCUMENT ME! * * @param g1 - * DOCUMENT ME! + * DOCUMENT ME! * @param startRes - * DOCUMENT ME! + * DOCUMENT ME! * @param endRes - * DOCUMENT ME! + * DOCUMENT ME! * @param startSeq - * DOCUMENT ME! + * DOCUMENT ME! * @param endSeq - * DOCUMENT ME! + * DOCUMENT ME! * @param offset - * DOCUMENT ME! + * DOCUMENT ME! */ void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, int endSeq, int offset) { - if (!av.hasHiddenColumns) + if (!av.hasHiddenColumns()) { draw(g1, startRes, endRes, startSeq, endSeq, offset); } @@ -633,7 +634,7 @@ public class SeqCanvas extends JComponent int blockStart = startRes; int blockEnd = endRes; - for (int i = 0; regions!=null && i < regions.size(); i++) + for (int i = 0; regions != null && i < regions.size(); i++) { int[] region = (int[]) regions.elementAt(i); int hideStart = region[0]; @@ -655,11 +656,9 @@ public class SeqCanvas extends JComponent { g1.setColor(Color.blue); - g1 - .drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, - 0 + offset, (blockEnd - blockStart + 1) - * av.charWidth - 1, (endSeq - startSeq) - * av.charHeight + offset); + g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, + 0 + offset, (blockEnd - blockStart + 1) * av.charWidth + - 1, (endSeq - startSeq) * av.charHeight + offset); } g1.translate(-screenY * av.charWidth, 0); @@ -693,13 +692,14 @@ public class SeqCanvas extends JComponent // /////////////////////////// for (int i = startSeq; i < endSeq; i++) { - nextSeq = av.alignment.getSequenceAt(i); - if (nextSeq==null) + nextSeq = av.getAlignment().getSequenceAt(i); + if (nextSeq == null) { - // occasionally, a race condition occurs such that the alignment row is empty + // occasionally, a race condition occurs such that the alignment row is + // empty continue; } - sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), + sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), startRes, endRes, offset + ((i - startSeq) * av.charHeight)); if (av.showSequenceFeatures) @@ -736,7 +736,7 @@ public class SeqCanvas extends JComponent } if (av.getSelectionGroup() != null - || av.alignment.getGroups().size() > 0) + || av.getAlignment().getGroups().size() > 0) { drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); } @@ -759,9 +759,9 @@ public class SeqCanvas extends JComponent int groupIndex = -1; int visWidth = (endRes - startRes + 1) * av.charWidth; - if ((group == null) && (av.alignment.getGroups().size() > 0)) + if ((group == null) && (av.getAlignment().getGroups().size() > 0)) { - group = (SequenceGroup) av.alignment.getGroups().elementAt(0); + group = (SequenceGroup) av.getAlignment().getGroups().get(0); groupIndex = 0; } @@ -788,11 +788,11 @@ public class SeqCanvas extends JComponent if ((sx <= (endRes - startRes) * av.charWidth) && group.getSequences(null).contains( - av.alignment.getSequenceAt(i))) + av.getAlignment().getSequenceAt(i))) { if ((bottom == -1) && !group.getSequences(null).contains( - av.alignment.getSequenceAt(i + 1))) + av.getAlignment().getSequenceAt(i + 1))) { bottom = sy + av.charHeight; } @@ -801,7 +801,7 @@ public class SeqCanvas extends JComponent { if (((top == -1) && (i == 0)) || !group.getSequences(null).contains( - av.alignment.getSequenceAt(i - 1))) + av.getAlignment().getSequenceAt(i - 1))) { top = sy; } @@ -917,15 +917,15 @@ public class SeqCanvas extends JComponent g.setStroke(new BasicStroke()); - if (groupIndex >= av.alignment.getGroups().size()) + if (groupIndex >= av.getAlignment().getGroups().size()) { break; } - group = (SequenceGroup) av.alignment.getGroups().elementAt( - groupIndex); + group = (SequenceGroup) av.getAlignment().getGroups() + .get(groupIndex); - } while (groupIndex < av.alignment.getGroups().size()); + } while (groupIndex < av.getAlignment().getGroups().size()); } @@ -935,7 +935,7 @@ public class SeqCanvas extends JComponent * DOCUMENT ME! * * @param results - * DOCUMENT ME! + * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) {