X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=36a4575e784cf274252c1fdc274561943f99e7e2;hb=51728d3951398f9c12d7017c776953f17322cc68;hp=360bcbf8d70c65b1371869f9ac99402f65ab4fdf;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 360bcbf..36a4575 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,27 +1,38 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 java.awt.*; -import java.awt.event.*; -import java.awt.image.*; -import javax.swing.*; +import jalview.renderer.AnnotationRenderer; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Graphics; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.event.MouseMotionAdapter; +import java.awt.image.BufferedImage; + +import javax.swing.JPanel; /** * DOCUMENT ME! @@ -37,6 +48,8 @@ public class OverviewPanel extends JPanel implements Runnable AlignmentPanel ap; + final AnnotationRenderer renderer = new AnnotationRenderer(); + float scalew = 1f; float scaleh = 1f; @@ -61,13 +74,13 @@ public class OverviewPanel extends JPanel implements Runnable // main visible SeqCanvas SequenceRenderer sr; - FeatureRenderer fr; + jalview.renderer.seqfeatures.FeatureRenderer fr; /** * Creates a new OverviewPanel object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! */ public OverviewPanel(AlignmentPanel ap) { @@ -81,15 +94,15 @@ 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 +126,7 @@ public class OverviewPanel extends JPanel implements Runnable addComponentListener(new ComponentAdapter() { + @Override public void componentResized(ComponentEvent evt) { if ((getWidth() != width) @@ -125,10 +139,13 @@ public class OverviewPanel extends JPanel implements Runnable addMouseMotionListener(new MouseMotionAdapter() { + @Override public void mouseDragged(MouseEvent evt) { - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { + // TODO: feature: jv2.5 detect shift drag and update selection from + // it. boxX = evt.getX(); boxY = evt.getY(); checkValid(); @@ -138,9 +155,10 @@ public class OverviewPanel extends JPanel implements Runnable addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { boxX = evt.getX(); boxY = evt.getY(); @@ -174,7 +192,7 @@ 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 +203,7 @@ 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 +213,10 @@ 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); @@ -238,18 +256,19 @@ public class OverviewPanel extends JPanel implements Runnable /** * DOCUMENT ME! */ + @Override public void run() { miniMe = null; - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { - fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); + fr.transferSettings(ap.getSeqPanel().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)); @@ -273,15 +292,28 @@ public class OverviewPanel extends JPanel implements Runnable int color = Color.white.getRGB(); int row, col; jalview.datamodel.SequenceI seq; + final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av + .hasHiddenColumns(); boolean hiddenRow = false; + // get hidden row and hidden column map once at beginning. + // clone featureRenderer settings to avoid race conditions... if state is + // updated just need to refresh again for (row = 0; row < sequencesHeight; row++) { + if (resizeAgain) + { + break; + } if ((int) (row * sampleRow) == lastrow) { // No need to recalculate the colours, // Just copy from the row above for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1)); } continue; @@ -290,15 +322,16 @@ public class OverviewPanel extends JPanel implements Runnable lastrow = (int) (row * sampleRow); hiddenRow = false; - if (av.hasHiddenRows) + if (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 +340,7 @@ public class OverviewPanel extends JPanel implements Runnable } else { - seq = av.alignment.getSequenceAt(lastrow); + seq = av.getAlignment().getSequenceAt(lastrow); } if (seq == null) @@ -316,8 +349,13 @@ public class OverviewPanel extends JPanel implements Runnable continue; } + // long start = System.currentTimeMillis(); for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } if ((int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow) { @@ -331,7 +369,7 @@ public class OverviewPanel extends JPanel implements Runnable { color = sr.getResidueBoxColour(seq, lastcol).getRGB(); - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { color = fr.findFeatureColour(color, seq, lastcol); } @@ -342,8 +380,8 @@ public class OverviewPanel extends JPanel implements Runnable } if (hiddenRow - || (av.hasHiddenColumns && !av.getColumnSelection() - .isVisible(lastcol))) + || (hasHiddenCols && !av.getColumnSelection().isVisible( + lastcol))) { color = new Color(color).darker().darker().getRGB(); } @@ -351,16 +389,24 @@ public class OverviewPanel extends JPanel implements Runnable miniMe.setRGB(col, row, color); } + // System.out.println(String.format("Row %d with width %d took %dms", + // row, width, System.currentTimeMillis() - start)); } - if (av.conservation != null) + if (av.getAlignmentConservationAnnotation() != null) { + renderer.updateFromAlignViewport(av); for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } 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); @@ -371,13 +417,17 @@ public class OverviewPanel extends JPanel implements Runnable resizing = false; - setBoxPosition(); - if (resizeAgain) { resizeAgain = false; updateOverviewImage(); } + else + { + lastMiniMe = miniMe; + } + + setBoxPosition(); } /** @@ -385,15 +435,15 @@ 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 +452,12 @@ 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 +468,7 @@ 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); } @@ -432,27 +482,43 @@ public class OverviewPanel extends JPanel implements Runnable repaint(); } + private BufferedImage lastMiniMe = null; + /** * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { - if (resizing) + if (resizing || resizeAgain) { - g.setColor(Color.white); + if (lastMiniMe == null) + { + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); + } + else + { + g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + } + g.setColor(new Color(100, 100, 100, 25)); g.fillRect(0, 0, getWidth(), getHeight()); } - else if (miniMe != null) + else if (lastMiniMe != null) { - g.drawImage(miniMe, 0, 0, this); + g.drawImage(lastMiniMe, 0, 0, this); + if (lastMiniMe != miniMe) + { + g.setColor(new Color(100, 100, 100, 25)); + g.fillRect(0, 0, getWidth(), getHeight()); + } } - + // TODO: render selected regions g.setColor(Color.red); g.drawRect(boxX, boxY, boxWidth, boxHeight); g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2); - } }