From aa6643d51133a8541dcbe30191b344aa09907a5f Mon Sep 17 00:00:00 2001 From: kiramt Date: Thu, 9 Feb 2017 13:00:32 +0000 Subject: [PATCH] JAL-2388 Initial refactor of OverviewPanel --- src/jalview/api/AlignViewportI.java | 6 + src/jalview/appletgui/OverviewPanel.java | 425 ++++++++++-------------- src/jalview/gui/OverviewPanel.java | 436 +++++++++---------------- src/jalview/viewmodel/AlignmentViewport.java | 3 + src/jalview/viewmodel/OverviewDimensions.java | 291 +++++++++++++++++ 5 files changed, 621 insertions(+), 540 deletions(-) create mode 100644 src/jalview/viewmodel/OverviewDimensions.java diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 72542b3..9e080a0 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -47,6 +47,8 @@ public interface AlignViewportI extends ViewStyleI int getEndRes(); + int getStartRes(); + /** * calculate the height for visible annotation, revalidating bounds where * necessary ABSTRACT GUI METHOD @@ -445,4 +447,8 @@ public interface AlignViewportI extends ViewStyleI * @return search results or null */ SearchResultsI getSearchResults(); + + int getStartSeq(); + + int getEndSeq(); } diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 9b2be4c..743d217 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -20,7 +20,7 @@ */ package jalview.appletgui; -import jalview.datamodel.AlignmentI; +import jalview.viewmodel.OverviewDimensions; import java.awt.Color; import java.awt.Dimension; @@ -37,33 +37,29 @@ import java.awt.event.MouseMotionListener; public class OverviewPanel extends Panel implements Runnable, MouseMotionListener, MouseListener { - Image miniMe; + private OverviewDimensions od; - Image offscreen; + private Image miniMe; - AlignViewport av; + private Image offscreen; - AlignmentPanel ap; + private AlignViewport av; - float scalew = 1f; + private AlignmentPanel ap; - float scaleh = 1f; + private boolean resizing = false; - public int width, sequencesHeight; - - int graphHeight = 20; - - int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1; - - boolean resizing = false; + // This is set true if the user resizes whilst + // the overview is being calculated + private boolean resizeAgain = false; // Can set different properties in this seqCanvas than // main visible SeqCanvas - SequenceRenderer sr; + private SequenceRenderer sr; - FeatureRenderer fr; + private FeatureRenderer fr; - Frame nullFrame; + private Frame nullFrame; public OverviewPanel(AlignmentPanel ap) { @@ -79,45 +75,17 @@ public class OverviewPanel extends Panel implements Runnable, sr.forOverview = true; fr = new FeatureRenderer(av); - // scale the initial size of overviewpanel to shape of alignment - float initialScale = (float) av.getAlignment().getWidth() - / (float) av.getAlignment().getHeight(); + od = new OverviewDimensions(av); - if (av.getSequenceConsensusHash() == null) - { - graphHeight = 0; - } - - if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) - { - // wider - width = 400; - sequencesHeight = (int) (400f / initialScale); - if (sequencesHeight < 40) - { - sequencesHeight = 40; - } - } - else - { - // taller - width = (int) (400f * initialScale); - sequencesHeight = 300; - if (width < 120) - { - width = 120; - } - } - - setSize(new Dimension(width, sequencesHeight + graphHeight)); + setSize(new Dimension(od.getWidth(), od.getHeight())); addComponentListener(new ComponentAdapter() { @Override public void componentResized(ComponentEvent evt) { - if (getSize().width != width - || getSize().height != sequencesHeight + graphHeight) + if ((getWidth() != od.getWidth()) + || (getHeight() != (od.getHeight()))) { updateOverviewImage(); } @@ -155,74 +123,34 @@ public class OverviewPanel extends Panel implements Runnable, @Override public void mousePressed(MouseEvent evt) { - boxX = evt.getX(); - boxY = evt.getY(); + od.setBoxX(evt.getX()); + od.setBoxY(evt.getY()); checkValid(); } @Override public void mouseReleased(MouseEvent evt) { - boxX = evt.getX(); - boxY = evt.getY(); + od.setBoxX(evt.getX()); + od.setBoxY(evt.getY()); checkValid(); } @Override public void mouseDragged(MouseEvent evt) { - boxX = evt.getX(); - boxY = evt.getY(); + od.setBoxX(evt.getX()); + od.setBoxY(evt.getY()); checkValid(); } - void checkValid() + /** + * Check box dimensions and scroll positions and correct if necessary + */ + private void checkValid() { - if (boxY < 0) - { - boxY = 0; - } - - if (boxY > (sequencesHeight - boxHeight)) - { - boxY = sequencesHeight - boxHeight + 1; - } - - if (boxX < 0) - { - boxX = 0; - } - - if (boxX > (width - boxWidth)) - { - if (av.hasHiddenColumns()) - { - // Try smallest possible box - boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew); - } - boxX = width - boxWidth; - } - - int col = (int) (boxX / scalew / av.getCharWidth()); - int row = (int) (boxY / scaleh / av.getCharHeight()); - - if (av.hasHiddenColumns()) - { - if (!av.getColumnSelection().isVisible(col)) - { - return; - } - - col = av.getColumnSelection().findColumnPosition(col); - } - - if (av.hasHiddenRows()) - { - row = av.getAlignment().getHiddenSequences() - .findIndexWithoutHiddenSeqs(row); - } - - ap.setScrollValues(col, row); + od.checkValid(); + ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); ap.paintAlignment(false); } @@ -244,29 +172,22 @@ public class OverviewPanel extends Panel implements Runnable, resizing = true; - if ((getSize().width > 0) && (getSize().height > 0)) + if ((getWidth() > 0) && (getHeight() > 0)) { - width = getSize().width; - sequencesHeight = getSize().height - graphHeight; + od.setWidth(getWidth()); // width = getWidth(); + od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight; } - setSize(new Dimension(width, sequencesHeight + graphHeight)); + setSize(new Dimension(od.getWidth(), od.getHeight())); Thread thread = new Thread(this); thread.start(); repaint(); } - // This is set true if the user resizes whilst - // the overview is being calculated - boolean resizeAgain = false; - @Override public void run() { miniMe = null; - int alwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getHeight() - + av.getAlignment().getHiddenSequences().getSize(); if (av.isShowSequenceFeatures()) { @@ -275,135 +196,38 @@ public class OverviewPanel extends Panel implements Runnable, if (getSize().width > 0 && getSize().height > 0) { - width = getSize().width; - sequencesHeight = getSize().height - graphHeight; + od.setWidth(getSize().width); + od.setHeight(getSize().height - od.getGraphHeight()); } - setSize(new Dimension(width, sequencesHeight + graphHeight)); - - int fullsizeWidth = alwidth * av.getCharWidth(); - int fullsizeHeight = alheight * av.getCharHeight(); + setSize(new Dimension(od.getWidth(), od.getHeight())); - scalew = (float) width / (float) fullsizeWidth; - scaleh = (float) sequencesHeight / (float) fullsizeHeight; - - miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight); - offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight); + miniMe = nullFrame.createImage(od.getWidth(), od.getHeight()); + offscreen = nullFrame.createImage(od.getWidth(), od.getHeight()); Graphics mg = miniMe.getGraphics(); - float sampleCol = (float) alwidth / (float) width; - float sampleRow = (float) alheight / (float) sequencesHeight; - int lastcol = 0, lastrow = 0; - int xstart = 0, ystart = 0; - 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++; - continue; - } - - hiddenRow = false; - if (hasHiddenRows) - { - seq = alignment.getHiddenSequences().getHiddenSequence(lastrow); - if (seq == null) - { - int index = alignment.getHiddenSequences() - .findIndexWithoutHiddenSeqs(lastrow); - - seq = alignment.getSequenceAt(index); - } - else - { - hiddenRow = true; - } - } - else - { - seq = alignment.getSequenceAt(lastrow); - } + od.updateScales(); - for (col = 0; col < width; col++) - { - if ((int) (col * sampleCol) == lastcol - && (int) (row * sampleRow) == lastrow) - { - sameCol++; - continue; - } - - lastcol = (int) (col * sampleCol); - - if (seq.getLength() > lastcol) - { - color = sr.getResidueBoxColour(seq, lastcol); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - else - { - color = Color.white; // White - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection().isVisible( - lastcol))) - { - color = color.darker().darker(); - } - - mg.setColor(color); - if (sameCol == 1 && sameRow == 1) - { - mg.drawLine(xstart, ystart, xstart, ystart); - } - else - { - mg.fillRect(xstart, ystart, sameCol, sameRow); - } + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight() + + av.getAlignment().getHiddenSequences().getSize(); + float sampleCol = alwidth / (float) od.getWidth(); + float sampleRow = alheight / (float) od.getSequencesHeight(); - xstart = col; - sameCol = 1; - } - lastrow = (int) (row * sampleRow); - ystart = row; - sameRow = 1; - } + buildImage(sampleRow, sampleCol, mg); if (av.getAlignmentConservationAnnotation() != null) { - for (col = 0; col < width; col++) + for (int col = 0; col < od.getWidth() && !resizeAgain; col++) { - if (resizeAgain) - { - break; - } - lastcol = (int) (col * sampleCol); - { - mg.translate(col, sequencesHeight); - 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); - } + mg.translate(col, od.getSequencesHeight()); + ap.annotationPanel.renderer.drawGraph(mg, + av.getAlignmentConservationAnnotation(), + av.getAlignmentConservationAnnotation().annotations, + (int) (sampleCol) + 1, od.getGraphHeight(), + (int) (col * sampleCol), (int) (col * sampleCol) + 1); + mg.translate(-col, -od.getSequencesHeight()); } } System.gc(); @@ -419,52 +243,129 @@ public class OverviewPanel extends Panel implements Runnable, } } - public void setBoxPosition() + private void buildImage(float sampleRow, float sampleCol, Graphics mg) { - 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()) - { - startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); - endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); - } + int lastcol = 0; + int lastrow = 0; + int xstart = 0; + int ystart = 0; + Color color = Color.yellow; + int sameRow = 0; + int sameCol = 0; - int startSeq = av.startSeq; - int endSeq = av.endSeq; + jalview.datamodel.SequenceI seq = null; + final boolean hasHiddenRows = av.hasHiddenRows(); + final boolean hasHiddenCols = av.hasHiddenColumns(); + boolean hiddenRow = false; - if (av.hasHiddenRows()) + for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++) { - startSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(startSeq); + if ((int) (row * sampleRow) == lastrow) + { + sameRow++; + continue; + } + else + { + // this should largely be a method in Alignment + hiddenRow = false; + if (hasHiddenRows) + { + seq = av.getAlignment().getHiddenSequences() + .getHiddenSequence(lastrow); + if (seq == null) + { + int index = av.getAlignment().getHiddenSequences() + .findIndexWithoutHiddenSeqs(lastrow); - endSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(endSeq); + seq = av.getAlignment().getSequenceAt(index); + } + else + { + hiddenRow = true; + } + } + else + { + seq = av.getAlignment().getSequenceAt(lastrow); + } + // end of Alignment method + for (int col = 0; col < od.getWidth(); col++) + { + if ((int) (col * sampleCol) == lastcol + && (int) (row * sampleRow) == lastrow) + { + sameCol++; + } + else + { + lastcol = (int) (col * sampleCol); + + color = getColumnColourFromSequence(seq, hiddenRow, + hasHiddenCols, lastcol); + + mg.setColor(color); + if (sameCol == 1 && sameRow == 1) + { + mg.drawLine(xstart, ystart, xstart, ystart); + } + else + { + mg.fillRect(xstart, ystart, sameCol, sameRow); + } + + xstart = col; + sameCol = 1; + } + } + lastrow = (int) (row * sampleRow); + ystart = row; + sameRow = 1; + } } - scalew = (float) width / (float) fullsizeWidth; - scaleh = (float) sequencesHeight / (float) fullsizeHeight; - - boxX = (int) (startRes * av.getCharWidth() * scalew); - boxY = (int) (startSeq * av.getCharHeight() * scaleh); + } - if (av.hasHiddenColumns()) + /* + * Find the colour of a sequence at a specified column position + */ + private Color getColumnColourFromSequence( + jalview.datamodel.SequenceI seq, boolean hiddenRow, + boolean hasHiddenCols, int lastcol) + { + Color color; + if (seq.getLength() > lastcol) { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); + color = sr.getResidueBoxColour(seq, lastcol); + + if (av.isShowSequenceFeatures()) + { + color = fr.findFeatureColour(color, seq, lastcol); + } } else { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); + color = Color.white; // White } - boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh); + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection() + .isVisible(lastcol))) + { + color = color.darker().darker(); + } + return color; + } + /** + * Update the overview panel box when the associated alignment panel is + * changed + * + */ + public void setBoxPosition() + { + od.setBoxPosition(); repaint(); } @@ -482,8 +383,10 @@ public class OverviewPanel extends Panel implements Runnable, { og.drawImage(miniMe, 0, 0, this); og.setColor(Color.red); - og.drawRect(boxX, boxY, boxWidth, boxHeight); - og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2); + og.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(), + od.getBoxHeight()); + og.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2, + od.getBoxHeight() - 2); g.drawImage(offscreen, 0, 0, this); } } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 1c48690..fc3cc4b 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.renderer.AnnotationRenderer; +import jalview.viewmodel.OverviewDimensions; import java.awt.Color; import java.awt.Dimension; @@ -42,45 +43,38 @@ import javax.swing.JPanel; */ public class OverviewPanel extends JPanel implements Runnable { - BufferedImage miniMe; + private static final Color TRANS_GREY = new Color(100, 100, 100, 25); - AlignViewport av; + private final AnnotationRenderer renderer = new AnnotationRenderer(); - AlignmentPanel ap; + private OverviewDimensions od; - final AnnotationRenderer renderer = new AnnotationRenderer(); + private BufferedImage miniMe; - float scalew = 1f; - - float scaleh = 1f; - - int width; - - int sequencesHeight; - - int graphHeight = 20; - - int boxX = -1; + private BufferedImage lastMiniMe = null; - int boxY = -1; + private AlignViewport av; - int boxWidth = -1; + private AlignmentPanel ap; - int boxHeight = -1; + // + private boolean resizing = false; - boolean resizing = false; + // This is set true if the user resizes whilst + // the overview is being calculated + private boolean resizeAgain = false; // Can set different properties in this seqCanvas than // main visible SeqCanvas - SequenceRenderer sr; + private SequenceRenderer sr; - jalview.renderer.seqfeatures.FeatureRenderer fr; + private jalview.renderer.seqfeatures.FeatureRenderer fr; /** * Creates a new OverviewPanel object. * * @param ap - * DOCUMENT ME! + * The alignment panel which is shown in the overview panel */ public OverviewPanel(AlignmentPanel ap) { @@ -93,44 +87,15 @@ public class OverviewPanel extends JPanel implements Runnable sr.forOverview = true; fr = new FeatureRenderer(ap); - // scale the initial size of overviewpanel to shape of alignment - float initialScale = (float) av.getAlignment().getWidth() - / (float) av.getAlignment().getHeight(); - - if (av.getAlignmentConservationAnnotation() == null) - { - graphHeight = 0; - } - - if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) - { - // wider - width = 400; - sequencesHeight = (int) (400f / initialScale); - if (sequencesHeight < 40) - { - sequencesHeight = 40; - } - } - else - { - // taller - width = (int) (400f * initialScale); - sequencesHeight = 300; - - if (width < 120) - { - width = 120; - } - } + od = new OverviewDimensions(av); addComponentListener(new ComponentAdapter() { @Override public void componentResized(ComponentEvent evt) { - if ((getWidth() != width) - || (getHeight() != (sequencesHeight + graphHeight))) + if ((getWidth() != od.getWidth()) + || (getHeight() != (od.getHeight()))) { updateOverviewImage(); } @@ -146,8 +111,8 @@ public class OverviewPanel extends JPanel implements Runnable { // TODO: feature: jv2.5 detect shift drag and update selection from // it. - boxX = evt.getX(); - boxY = evt.getY(); + od.setBoxX(evt.getX()); + od.setBoxY(evt.getY()); checkValid(); } } @@ -160,8 +125,8 @@ public class OverviewPanel extends JPanel implements Runnable { if (!av.getWrapAlignment()) { - boxX = evt.getX(); - boxY = evt.getY(); + od.setBoxX(evt.getX()); + od.setBoxY(evt.getY()); checkValid(); } } @@ -171,60 +136,17 @@ public class OverviewPanel extends JPanel implements Runnable } /** - * DOCUMENT ME! + * Check box dimensions and scroll positions and correct if necessary */ - void checkValid() + private void checkValid() { - if (boxY < 0) - { - boxY = 0; - } - - if (boxY > (sequencesHeight - boxHeight)) - { - boxY = sequencesHeight - boxHeight + 1; - } - - if (boxX < 0) - { - boxX = 0; - } - - if (boxX > (width - boxWidth)) - { - if (av.hasHiddenColumns()) - { - // Try smallest possible box - boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew); - } - boxX = width - boxWidth; - } - - int col = (int) (boxX / scalew / av.getCharWidth()); - int row = (int) (boxY / scaleh / av.getCharHeight()); - - if (av.hasHiddenColumns()) - { - if (!av.getColumnSelection().isVisible(col)) - { - return; - } - - col = av.getColumnSelection().findColumnPosition(col); - } - - if (av.hasHiddenRows()) - { - row = av.getAlignment().getHiddenSequences() - .findIndexWithoutHiddenSeqs(row); - } - - ap.setScrollValues(col, row); + od.checkValid(); + ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); } /** - * DOCUMENT ME! + * Updates the overview image when the related alignment panel is updated */ public void updateOverviewImage() { @@ -238,24 +160,17 @@ public class OverviewPanel extends JPanel implements Runnable if ((getWidth() > 0) && (getHeight() > 0)) { - width = getWidth(); - sequencesHeight = getHeight() - graphHeight; + od.setWidth(getWidth()); // width = getWidth(); + od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight; } - setPreferredSize(new Dimension(width, sequencesHeight + graphHeight)); + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); Thread thread = new Thread(this); thread.start(); repaint(); } - // This is set true if the user resizes whilst - // the overview is being calculated - boolean resizeAgain = false; - - /** - * DOCUMENT ME! - */ @Override public void run() { @@ -266,81 +181,114 @@ public class OverviewPanel extends JPanel implements Runnable fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); } + // why do we need to set preferred size again? was set in + // updateOverviewImage + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); + + miniMe = new BufferedImage(od.getWidth(), od.getHeight(), + BufferedImage.TYPE_INT_RGB); + + Graphics mg = miniMe.getGraphics(); + mg.setColor(Color.orange); + mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight()); + + // calculate scale based on current alignment width and height + od.updateScales(); + + // calculate sampleCol and sampleRow + // alignment width is max number of residues/bases + // alignment height is number of sequences int alwidth = av.getAlignment().getWidth(); int alheight = av.getAlignment().getHeight() + av.getAlignment().getHiddenSequences().getSize(); - setPreferredSize(new Dimension(width, sequencesHeight + graphHeight)); + // sampleCol or sampleRow is the width/height allocated to each residue + // in particular, sometimes we may need more than one row/col of the + // BufferedImage allocated + // sampleCol is how much of a residue to assign to each pixel + // sampleRow is how many sequences to assign to each pixel + float sampleCol = alwidth / (float) od.getWidth(); + float sampleRow = alheight / (float) od.getSequencesHeight(); + + buildImage(sampleRow, sampleCol); - int fullsizeWidth = alwidth * av.getCharWidth(); - int fullsizeHeight = alheight * av.getCharHeight(); + if (av.getAlignmentConservationAnnotation() != null) + { + renderer.updateFromAlignViewport(av); + for (int col = 0; col < od.getWidth() && !resizeAgain; col++) + { + mg.translate(col, od.getSequencesHeight()); + renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), + av.getAlignmentConservationAnnotation().annotations, + (int) (sampleCol) + 1, od.getGraphHeight(), + (int) (col * sampleCol), (int) (col * sampleCol) + 1); + mg.translate(-col, -od.getSequencesHeight()); - scalew = (float) width / (float) fullsizeWidth; - scaleh = (float) sequencesHeight / (float) fullsizeHeight; + } + } + System.gc(); - miniMe = new BufferedImage(width, sequencesHeight + graphHeight, - BufferedImage.TYPE_INT_RGB); + resizing = false; - Graphics mg = miniMe.getGraphics(); - mg.setColor(Color.orange); - mg.fillRect(0, 0, width, miniMe.getHeight()); + if (resizeAgain) + { + resizeAgain = false; + updateOverviewImage(); + } + else + { + lastMiniMe = miniMe; + } - float sampleCol = (float) alwidth / (float) width; - float sampleRow = (float) alheight / (float) sequencesHeight; + setBoxPosition(); + } - int lastcol = -1, lastrow = -1; + private void buildImage(float sampleRow, float sampleCol) + { + int lastcol = -1; + int lastrow = -1; int color = Color.white.getRGB(); - int row, col; - jalview.datamodel.SequenceI seq; - final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av - .hasHiddenColumns(); + + jalview.datamodel.SequenceI seq = null; + final boolean hasHiddenRows = av.hasHiddenRows(); + final boolean 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++) + for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++) { - if (resizeAgain) + boolean doCopy = true; + int currentrow = (int) (row * sampleRow); + if (currentrow != lastrow) { - 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; - } + doCopy = false; - lastrow = (int) (row * sampleRow); + lastrow = currentrow; - hiddenRow = false; - if (hasHiddenRows) - { - seq = av.getAlignment().getHiddenSequences() - .getHiddenSequence(lastrow); - if (seq == null) + hiddenRow = false; + // should be method(s) in Alignment + if (hasHiddenRows) { - int index = av.getAlignment().getHiddenSequences() - .findIndexWithoutHiddenSeqs(lastrow); + seq = av.getAlignment().getHiddenSequences() + .getHiddenSequence(lastrow); + if (seq == null) + { + int index = av.getAlignment().getHiddenSequences() + .findIndexWithoutHiddenSeqs(lastrow); - seq = av.getAlignment().getSequenceAt(index); + seq = av.getAlignment().getSequenceAt(index); + } + else + { + hiddenRow = true; + } } else { - hiddenRow = true; + seq = av.getAlignment().getSequenceAt(lastrow); } - } - else - { - seq = av.getAlignment().getSequenceAt(lastrow); + // end of Alignment method(s) } if (seq == null) @@ -349,144 +297,72 @@ public class OverviewPanel extends JPanel implements Runnable continue; } - for (col = 0; col < width; col++) + for (int col = 0; col < od.getWidth() && !resizeAgain; col++) { - if (resizeAgain) - { - break; - } - if ((int) (col * sampleCol) == lastcol - && (int) (row * sampleRow) == lastrow) + if (doCopy) { - miniMe.setRGB(col, row, color); - continue; + color = miniMe.getRGB(col, row - 1); } - - lastcol = (int) (col * sampleCol); - - if (seq.getLength() > lastcol) - { - color = sr.getResidueBoxColour(seq, lastcol).getRGB(); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - else - { - color = -1; // White - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection().isVisible( - lastcol))) + else if ((int) (col * sampleCol) != lastcol + || (int) (row * sampleRow) != lastrow) { - color = new Color(color).darker().darker().getRGB(); + lastcol = (int) (col * sampleCol); + color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols, + lastcol); } + // else if ((int) (col * sampleCol) == lastcol && (int) (row * + // sampleRow) == lastrow)) + // we just use the color we already have , so don't need to set it miniMe.setRGB(col, row, color); - } } + } - if (av.getAlignmentConservationAnnotation() != null) + /* + * Find the colour of a sequence at a specified column position + */ + private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, + boolean hiddenRow, boolean hasHiddenCols, int lastcol) + { + int color; + + if (seq.getLength() > lastcol) { - renderer.updateFromAlignViewport(av); - for (col = 0; col < width; col++) + color = sr.getResidueBoxColour(seq, lastcol).getRGB(); + + if (av.isShowSequenceFeatures()) { - if (resizeAgain) - { - break; - } - lastcol = (int) (col * sampleCol); - { - mg.translate(col, sequencesHeight); - renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), - av.getAlignmentConservationAnnotation().annotations, - (int) (sampleCol) + 1, graphHeight, - (int) (col * sampleCol), (int) (col * sampleCol) + 1); - mg.translate(-col, -sequencesHeight); - } + color = fr.findFeatureColour(color, seq, lastcol); } } - System.gc(); - - resizing = false; - - if (resizeAgain) + else { - resizeAgain = false; - updateOverviewImage(); + color = Color.white.getRGB(); // White } - else + + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection() + .isVisible(lastcol))) { - lastMiniMe = miniMe; + color = new Color(color).darker().darker().getRGB(); } - setBoxPosition(); + return color; } /** - * DOCUMENT ME! + * Update the overview panel box when the associated alignment panel is + * changed + * */ public void setBoxPosition() { - 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()) - { - startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); - endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); - } - - int startSeq = av.startSeq; - int endSeq = av.endSeq; - - if (av.hasHiddenRows()) - { - startSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(startSeq); - - endSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(endSeq); - - } - - scalew = (float) width / (float) fullsizeWidth; - scaleh = (float) sequencesHeight / (float) fullsizeHeight; - - boxX = (int) (startRes * av.getCharWidth() * scalew); - boxY = (int) (startSeq * av.getCharHeight() * scaleh); - - if (av.hasHiddenColumns()) - { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); - } - else - { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); - } - - boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh); - + od.setBoxPosition(); repaint(); } - private BufferedImage lastMiniMe = null; - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - */ @Override public void paintComponent(Graphics g) { @@ -501,7 +377,7 @@ public class OverviewPanel extends JPanel implements Runnable { g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); } - g.setColor(new Color(100, 100, 100, 25)); + g.setColor(TRANS_GREY); g.fillRect(0, 0, getWidth(), getHeight()); } else if (lastMiniMe != null) @@ -509,13 +385,15 @@ public class OverviewPanel extends JPanel implements Runnable g.drawImage(lastMiniMe, 0, 0, this); if (lastMiniMe != miniMe) { - g.setColor(new Color(100, 100, 100, 25)); + g.setColor(TRANS_GREY); 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); + g.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(), + od.getBoxHeight()); + g.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2, + od.getBoxHeight() - 2); } } diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index fecccb0..0891071 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -2651,6 +2651,7 @@ public abstract class AlignmentViewport implements AlignViewportI, this.followHighlight = b; } + @Override public int getStartRes() { return startRes; @@ -2662,6 +2663,7 @@ public abstract class AlignmentViewport implements AlignViewportI, return endRes; } + @Override public int getStartSeq() { return startSeq; @@ -2705,6 +2707,7 @@ public abstract class AlignmentViewport implements AlignViewportI, this.endSeq = seq; } + @Override public int getEndSeq() { return endSeq; diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java new file mode 100644 index 0000000..17f56c9 --- /dev/null +++ b/src/jalview/viewmodel/OverviewDimensions.java @@ -0,0 +1,291 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.viewmodel; + +import jalview.api.AlignViewportI; + +public class OverviewDimensions +{ + // Default width and height values + private static final int DEFAULT_GRAPH_HEIGHT = 20; + + private static final int MAX_WIDTH = 400; + + private static final int MIN_WIDTH = 120; + + private static final int MIN_SEQ_HEIGHT = 40; + + private static final int MAX_SEQ_HEIGHT = 300; + + private AlignViewportI av; + + private float scalew = 1f; + + private float scaleh = 1f; + + // width of the overview panel + private int width; + + // height of sequences part of the overview panel + private int sequencesHeight; + + // height of the graphs part of the overview panel + private int graphHeight = DEFAULT_GRAPH_HEIGHT; + + // dimensions of box outlining current extent of view in alignment panel + // location of left side of box + private int boxX = -1; + + // location of bottom of box + private int boxY = -1; + + // width of box + private int boxWidth = -1; + + // height of box + private int boxHeight = -1; + + private int scrollCol = -1; + + private int scrollRow = -1; + + public OverviewDimensions(AlignViewportI avi) + { + this.av = avi; + + // scale the initial size of overviewpanel to shape of alignment + float initialScale = (float) av.getAlignment().getWidth() + / (float) av.getAlignment().getHeight(); + + // TODO: in applet this was getSequenceConsensusHash() + // check if it makes any functional difference + if (av.getAlignmentConservationAnnotation() == null) + { + graphHeight = 0; + } + + if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) + { + // wider + width = MAX_WIDTH; + sequencesHeight = (int) (MAX_WIDTH / initialScale); + if (sequencesHeight < MIN_SEQ_HEIGHT) + { + sequencesHeight = MIN_SEQ_HEIGHT; + } + } + else + { + // taller + width = (int) (MAX_WIDTH * initialScale); + sequencesHeight = MAX_SEQ_HEIGHT; + + if (width < MIN_WIDTH) + { + width = MIN_WIDTH; + } + } + } + + /** + * Check box dimensions and scroll positions and correct if necessary + */ + public void checkValid() + { + if (boxY < 0) + { + boxY = 0; + } + + if (boxY > (sequencesHeight - boxHeight)) + { + boxY = sequencesHeight - boxHeight + 1; + } + + if (boxX < 0) + { + boxX = 0; + } + + if (boxX > (width - boxWidth)) + { + if (av.hasHiddenColumns()) + { + // Try smallest possible box + boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1) + * av.getCharWidth() * scalew); + } + boxX = width - boxWidth; + } + + scrollCol = (int) (boxX / scalew / av.getCharWidth()); + scrollRow = (int) (boxY / scaleh / av.getCharHeight()); + + if (av.hasHiddenColumns()) + { + if (!av.getColumnSelection().isVisible(scrollCol)) + { + return; + } + + scrollCol = av.getColumnSelection().findColumnPosition(scrollCol); + } + + if (av.hasHiddenRows()) + { + scrollRow = av.getAlignment().getHiddenSequences() + .findIndexWithoutHiddenSeqs(scrollRow); + } + } + + /** + * Update the overview panel box when the associated alignment panel is + * changed + * + */ + public void setBoxPosition() + { + updateScales(); + + int startRes = av.getStartRes(); + int endRes = av.getEndRes(); + + if (av.hasHiddenColumns()) + { + startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); + endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); + } + + int startSeq = av.getStartSeq(); + int endSeq = av.getEndSeq(); + + if (av.hasHiddenRows()) + { + startSeq = av.getAlignment().getHiddenSequences() + .adjustForHiddenSeqs(startSeq); + + endSeq = av.getAlignment().getHiddenSequences() + .adjustForHiddenSeqs(endSeq); + + } + + boxX = (int) (startRes * av.getCharWidth() * scalew); + boxY = (int) (startSeq * av.getCharHeight() * scaleh); + + if (av.hasHiddenColumns()) + { + boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); + } + else + { + boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); + } + + boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh); + } + + /** + * Update width and height scales in terms of the alignment width and height + */ + public void updateScales() + { + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight() + + av.getAlignment().getHiddenSequences().getSize(); + + int fullsizeWidth = alwidth * av.getCharWidth(); + int fullsizeHeight = alheight * av.getCharHeight(); + + scalew = (float) width / fullsizeWidth; + scaleh = (float) sequencesHeight / fullsizeHeight; + } + + // don't like this, scroll vals are separate from setting code + public int getScrollCol() + { + return scrollCol; + } + + public int getScrollRow() + { + return scrollRow; + } + + public int getBoxX() + { + return boxX; + } + + public int getBoxY() + { + return boxY; + } + + public int getBoxWidth() + { + return boxWidth; + } + + public int getBoxHeight() + { + return boxHeight; + } + + public void setBoxX(int x) + { + boxX = x; + } + + public void setBoxY(int y) + { + boxY = y; + } + + public void setWidth(int w) + { + width = w; + } + + public void setHeight(int h) + { + sequencesHeight = h - graphHeight; + } + + public int getWidth() + { + return width; + } + + public int getHeight() + { + return sequencesHeight + graphHeight; + } + + public int getSequencesHeight() + { + return sequencesHeight; + } + + public int getGraphHeight() + { + return graphHeight; + } +} -- 1.7.10.2