X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=997491e5e8460dd7f84ea05cf090d398858b078f;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=6bc630c9a85c9b7626140028633c9db72b613fd6;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 6bc630c..997491e 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,23 +1,27 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * 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 + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; +import jalview.renderer.AnnotationRenderer; + import java.awt.*; import java.awt.event.*; import java.awt.image.*; @@ -37,6 +41,8 @@ public class OverviewPanel extends JPanel implements Runnable AlignmentPanel ap; + final AnnotationRenderer renderer = new AnnotationRenderer(); + float scalew = 1f; float scaleh = 1f; @@ -67,7 +73,7 @@ public class OverviewPanel extends JPanel implements Runnable * Creates a new OverviewPanel object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! */ public OverviewPanel(AlignmentPanel ap) { @@ -81,15 +87,15 @@ public class OverviewPanel extends JPanel implements Runnable fr = new FeatureRenderer(ap); // scale the initial size of overviewpanel to shape of alignment - float initialScale = (float) av.alignment.getWidth() - / (float) av.alignment.getHeight(); + float initialScale = (float) av.getAlignment().getWidth() + / (float) av.getAlignment().getHeight(); - if (av.conservation == null) + if (av.getAlignmentConservationAnnotation() == null) { graphHeight = 0; } - if (av.alignment.getWidth() > av.alignment.getHeight()) + if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) { // wider width = 400; @@ -113,6 +119,7 @@ public class OverviewPanel extends JPanel implements Runnable addComponentListener(new ComponentAdapter() { + @Override public void componentResized(ComponentEvent evt) { if ((getWidth() != width) @@ -125,10 +132,13 @@ public class OverviewPanel extends JPanel implements Runnable addMouseMotionListener(new MouseMotionAdapter() { + @Override public void mouseDragged(MouseEvent evt) { if (!av.wrapAlignment) { + // TODO: feature: jv2.5 detect shift drag and update selection from + // it. boxX = evt.getX(); boxY = evt.getY(); checkValid(); @@ -138,6 +148,7 @@ public class OverviewPanel extends JPanel implements Runnable addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (!av.wrapAlignment) @@ -174,7 +185,7 @@ public class OverviewPanel extends JPanel implements Runnable if (boxX > (width - boxWidth)) { - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { // Try smallest possible box boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew); @@ -185,7 +196,7 @@ public class OverviewPanel extends JPanel implements Runnable int col = (int) (boxX / scalew / av.getCharWidth()); int row = (int) (boxY / scaleh / av.getCharHeight()); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { if (!av.getColumnSelection().isVisible(col)) { @@ -195,10 +206,10 @@ public class OverviewPanel extends JPanel implements Runnable col = av.getColumnSelection().findColumnPosition(col); } - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs( - row); + row = av.getAlignment().getHiddenSequences() + .findIndexWithoutHiddenSeqs(row); } ap.setScrollValues(col, row); @@ -238,6 +249,7 @@ public class OverviewPanel extends JPanel implements Runnable /** * DOCUMENT ME! */ + @Override public void run() { miniMe = null; @@ -247,9 +259,9 @@ public class OverviewPanel extends JPanel implements Runnable fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); } - int alwidth = av.alignment.getWidth(); - int alheight = av.alignment.getHeight() - + av.alignment.getHiddenSequences().getSize(); + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight() + + av.getAlignment().getHiddenSequences().getSize(); setPreferredSize(new Dimension(width, sequencesHeight + graphHeight)); @@ -290,15 +302,16 @@ public class OverviewPanel extends JPanel implements Runnable lastrow = (int) (row * sampleRow); hiddenRow = false; - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow); + seq = av.getAlignment().getHiddenSequences() + .getHiddenSequence(lastrow); if (seq == null) { - int index = av.alignment.getHiddenSequences() + int index = av.getAlignment().getHiddenSequences() .findIndexWithoutHiddenSeqs(lastrow); - seq = av.alignment.getSequenceAt(index); + seq = av.getAlignment().getSequenceAt(index); } else { @@ -307,7 +320,7 @@ public class OverviewPanel extends JPanel implements Runnable } else { - seq = av.alignment.getSequenceAt(lastrow); + seq = av.getAlignment().getSequenceAt(lastrow); } if (seq == null) @@ -342,7 +355,7 @@ public class OverviewPanel extends JPanel implements Runnable } if (hiddenRow - || (av.hasHiddenColumns && !av.getColumnSelection() + || (av.hasHiddenColumns() && !av.getColumnSelection() .isVisible(lastcol))) { color = new Color(color).darker().darker().getRGB(); @@ -353,14 +366,16 @@ public class OverviewPanel extends JPanel implements Runnable } } - if (av.conservation != null) + if (av.getAlignmentConservationAnnotation() != null) { + renderer.updateFromAlignViewport(av); for (col = 0; col < width; col++) { lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); - ap.annotationPanel.drawGraph(mg, av.conservation, + renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), + av.getAlignmentConservationAnnotation().annotations, (int) (sampleCol) + 1, graphHeight, (int) (col * sampleCol), (int) (col * sampleCol) + 1); mg.translate(-col, -sequencesHeight); @@ -385,15 +400,15 @@ public class OverviewPanel extends JPanel implements Runnable */ public void setBoxPosition() { - int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth(); - int fullsizeHeight = (av.alignment.getHeight() + av.alignment + int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth(); + int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment() .getHiddenSequences().getSize()) * av.getCharHeight(); int startRes = av.getStartRes(); int endRes = av.getEndRes(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); @@ -402,12 +417,12 @@ public class OverviewPanel extends JPanel implements Runnable int startSeq = av.startSeq; int endSeq = av.endSeq; - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs( - startSeq); + startSeq = av.getAlignment().getHiddenSequences() + .adjustForHiddenSeqs(startSeq); - endSeq = av.alignment.getHiddenSequences() + endSeq = av.getAlignment().getHiddenSequences() .adjustForHiddenSeqs(endSeq); } @@ -418,7 +433,7 @@ public class OverviewPanel extends JPanel implements Runnable boxX = (int) (startRes * av.getCharWidth() * scalew); boxY = (int) (startSeq * av.getCharHeight() * scaleh); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); } @@ -436,8 +451,9 @@ public class OverviewPanel extends JPanel implements Runnable * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { if (resizing)