X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=9b2be4cd2975997ba091bceef62563912dcae7f3;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=ef7c16de437e40485b0105c92d81ae27bb3aa36f;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index ef7c16d..9b2be4c 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -1,25 +1,38 @@ /* - * 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 ($$Version-Rel$$) + * 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.appletgui; -import java.awt.*; -import java.awt.event.*; +import jalview.datamodel.AlignmentI; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Image; +import java.awt.Panel; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; public class OverviewPanel extends Panel implements Runnable, MouseMotionListener, MouseListener @@ -65,18 +78,17 @@ public class OverviewPanel extends Panel implements Runnable, sr.renderGaps = false; sr.forOverview = true; fr = new FeatureRenderer(av); - fr.overview = true; // 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.hconsensus == null) + if (av.getSequenceConsensusHash() == null) { graphHeight = 0; } - if (av.alignment.getWidth() > av.alignment.getHeight()) + if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) { // wider width = 400; @@ -101,6 +113,7 @@ public class OverviewPanel extends Panel implements Runnable, addComponentListener(new ComponentAdapter() { + @Override public void componentResized(ComponentEvent evt) { if (getSize().width != width @@ -119,22 +132,27 @@ public class OverviewPanel extends Panel implements Runnable, } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mouseMoved(MouseEvent evt) { } + @Override public void mousePressed(MouseEvent evt) { boxX = evt.getX(); @@ -142,6 +160,7 @@ public class OverviewPanel extends Panel implements Runnable, checkValid(); } + @Override public void mouseReleased(MouseEvent evt) { boxX = evt.getX(); @@ -149,6 +168,7 @@ public class OverviewPanel extends Panel implements Runnable, checkValid(); } + @Override public void mouseDragged(MouseEvent evt) { boxX = evt.getX(); @@ -175,7 +195,7 @@ public class OverviewPanel extends Panel 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); @@ -186,7 +206,7 @@ public class OverviewPanel extends Panel 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)) { @@ -196,10 +216,10 @@ public class OverviewPanel extends Panel 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); @@ -217,10 +237,9 @@ public class OverviewPanel extends Panel implements Runnable, return; } - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { - fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups; - fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours; + fr.transferSettings(ap.seqPanel.seqCanvas.fr); } resizing = true; @@ -241,13 +260,15 @@ public class OverviewPanel extends Panel implements Runnable, // the overview is being calculated boolean resizeAgain = false; + @Override public void run() { miniMe = null; - int alwidth = av.alignment.getWidth(); - int alheight = av.alignment.getHeight(); + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight() + + av.getAlignment().getHiddenSequences().getSize(); - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); } @@ -278,9 +299,16 @@ public class OverviewPanel extends Panel implements Runnable, Color color = Color.yellow; int row, col, sameRow = 0, sameCol = 0; jalview.datamodel.SequenceI seq; + final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av + .hasHiddenColumns(); boolean hiddenRow = false; + AlignmentI alignment = av.getAlignment(); for (row = 0; row <= sequencesHeight; row++) { + if (resizeAgain) + { + break; + } if ((int) (row * sampleRow) == lastrow) { sameRow++; @@ -288,15 +316,15 @@ public class OverviewPanel extends Panel implements Runnable, } hiddenRow = false; - if (av.hasHiddenRows) + if (hasHiddenRows) { - seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow); + seq = alignment.getHiddenSequences().getHiddenSequence(lastrow); if (seq == null) { - int index = av.alignment.getHiddenSequences() + int index = alignment.getHiddenSequences() .findIndexWithoutHiddenSeqs(lastrow); - seq = av.alignment.getSequenceAt(index); + seq = alignment.getSequenceAt(index); } else { @@ -305,7 +333,7 @@ public class OverviewPanel extends Panel implements Runnable, } else { - seq = av.alignment.getSequenceAt(lastrow); + seq = alignment.getSequenceAt(lastrow); } for (col = 0; col < width; col++) @@ -323,7 +351,7 @@ public class OverviewPanel extends Panel implements Runnable, { color = sr.getResidueBoxColour(seq, lastcol); - if (av.showSequenceFeatures) + if (av.isShowSequenceFeatures()) { color = fr.findFeatureColour(color, seq, lastcol); } @@ -334,8 +362,8 @@ public class OverviewPanel extends Panel implements Runnable, } if (hiddenRow - || (av.hasHiddenColumns && !av.getColumnSelection() - .isVisible(lastcol))) + || (hasHiddenCols && !av.getColumnSelection().isVisible( + lastcol))) { color = color.darker().darker(); } @@ -358,14 +386,20 @@ public class OverviewPanel extends Panel implements Runnable, sameRow = 1; } - if (av.conservation != null) + if (av.getAlignmentConservationAnnotation() != null) { for (col = 0; col < width; col++) { + if (resizeAgain) + { + break; + } lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); - ap.annotationPanel.drawGraph(mg, av.conservation, + ap.annotationPanel.renderer.drawGraph(mg, + av.getAlignmentConservationAnnotation(), + av.getAlignmentConservationAnnotation().annotations, (int) (sampleCol) + 1, graphHeight, (int) (col * sampleCol), (int) (col * sampleCol) + 1); mg.translate(-col, -sequencesHeight); @@ -387,15 +421,15 @@ public class OverviewPanel extends Panel 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); @@ -404,12 +438,12 @@ public class OverviewPanel extends Panel 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); } @@ -420,7 +454,7 @@ public class OverviewPanel extends Panel 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); } @@ -434,11 +468,13 @@ public class OverviewPanel extends Panel implements Runnable, repaint(); } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { Graphics og = offscreen.getGraphics();