From 298c2b85845dbaabda7e3304751cc856e7b0ad30 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 14 Oct 2011 12:37:36 +0100 Subject: [PATCH] (JAL-958) - normalised sequence logo for applet (JAL-826) - RNA stem annotation visualization for applet (Jalview 3) refactored Graphics2D annotation rendering to package shared by applet and application --- src/jalview/appletgui/AlignViewport.java | 77 ++- src/jalview/appletgui/AnnotationPanel.java | 670 +-------------------- src/jalview/appletgui/OverviewPanel.java | 2 +- src/jalview/gui/AlignViewport.java | 46 +- src/jalview/gui/AlignmentPanel.java | 2 +- src/jalview/gui/AnnotationPanel.java | 895 +--------------------------- src/jalview/gui/OverviewPanel.java | 6 +- src/jalview/gui/SeqCanvas.java | 2 +- 8 files changed, 176 insertions(+), 1524 deletions(-) diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 4d97720..9af5ac2 100644 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -22,14 +22,14 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; +import jalview.api.AlignViewportI; import jalview.bin.*; import jalview.datamodel.*; import jalview.schemes.*; import jalview.structure.SelectionSource; -import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; -public class AlignViewport implements SelectionSource, VamsasSource +public class AlignViewport implements AlignViewportI, SelectionSource, VamsasSource { int startRes; @@ -243,7 +243,9 @@ public class AlignViewport implements SelectionSource, VamsasSource followSelection = followHighlight; showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo); - + + normaliseSequenceLogo = applet.getDefaultParameter("normaliseSequenceLogo", normaliseSequenceLogo); + showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus); showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation); @@ -477,15 +479,22 @@ public class AlignViewport implements SelectionSource, VamsasSource ConservationThread conservationThread; ConsensusThread consensusThread; + +// StrucConsensusThread strucConsensusThread; + boolean consUpdateNeeded = false; static boolean UPDATING_CONSENSUS = false; + static boolean UPDATING_STRUC_CONSENSUS = false; + static boolean UPDATING_CONSERVATION = false; boolean updatingConsensus = false; + boolean updatingStrucConsensus = false; + boolean updatingConservation = false; /** @@ -1640,6 +1649,10 @@ public class AlignViewport implements SelectionSource, VamsasSource * should consensus profile be rendered by default */ public boolean showSequenceLogo = false; + /** + * should consensus profile be rendered normalised to row height + */ + public boolean normaliseSequenceLogo = false; /** * should consensus histograms be rendered by default @@ -1758,4 +1771,62 @@ public class AlignViewport implements SelectionSource, VamsasSource } } } + + @Override + public boolean hasHiddenColumns() + { + return hasHiddenColumns; + } + + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + + public boolean isCalcInProgress() + { + // TODO generalise to iterate over all calculators associated with av + return updatingConsensus || updatingConservation || updatingStrucConsensus; + } + + public boolean isCalculationInProgress( + AlignmentAnnotation alignmentAnnotation) + { + if (!alignmentAnnotation.autoCalculated) + return false; + if ((updatingConsensus && consensus==alignmentAnnotation) + || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation)) + // || (updatingStrucConsensus && strucConsensus==alignmentAnnotation) + ) + { + return true; + } + return false; + } + + /** + * + * @return true if alignment characters should be displayed + */ + public boolean isValidCharWidth() + { + return validCharWidth; + } + + @Override + public Hashtable[] getSequenceConsensusHash() + { + return hconsensus; + } + + @Override + public Hashtable[] getRnaStructureConsensusHash() + { + return null; // TODO: JAL-891 port to jvlite : refactor and introduce hStrucConsensus; + } } diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index d4fcf97..b61f1cb 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -26,9 +26,11 @@ import java.awt.geom.AffineTransform; import jalview.analysis.AAFrequency; import jalview.datamodel.*; +import jalview.renderer.AnnotationRenderer; +import jalview.renderer.AwtRenderPanelI; import jalview.schemes.ColourSchemeI; -public class AnnotationPanel extends Panel implements AdjustmentListener, +public class AnnotationPanel extends Panel implements AwtRenderPanelI, AdjustmentListener, ActionListener, MouseListener, MouseMotionListener { AlignViewport av; @@ -74,6 +76,8 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, boolean MAC = false; + public final AnnotationRenderer renderer; + public AnnotationPanel(AlignmentPanel ap) { MAC = new jalview.util.Platform().isAMac(); @@ -88,11 +92,13 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, addMouseListener(this); // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this ); + renderer = new AnnotationRenderer(); } public AnnotationPanel(AlignViewport av) { this.av = av; + renderer = new AnnotationRenderer(); } public void adjustmentValueChanged(AdjustmentEvent evt) @@ -624,664 +630,32 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, return; } - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - g.translate(0, -scrollOffset); - int x = 0; - int y = 0; - int column = 0; - char lastSS; - int lastSSX; - int iconOffset = av.charHeight / 2; - boolean validRes = false; - boolean validEnd = false; - boolean labelAllCols = false; - boolean centreColLabels, centreColLabelsDef = av - .getCentreColumnLabels(); - boolean scaleColLabel = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; - int charOffset = 0; // offset for a label - float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a - // column. - // \u03B2 \u03B1 - for (int i = 0; i < aa.length; i++) - { - AlignmentAnnotation row = aa[i]; - - if (!row.visible) - { - continue; - } - centreColLabels = row.centreColLabels || centreColLabelsDef; - labelAllCols = row.showAllColLabels; - scaleColLabel = row.scaleColLabel; - lastSS = ' '; - lastSSX = 0; - - if (row.graph > 0) - { - if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) - { - continue; - } - - // this is so that we draw the characters below the graph - y += row.height; - - if (row.hasText) - { - iconOffset = av.charHeight - fm.getDescent(); - y -= av.charHeight; - } - } - // TODO: else is the logic used in application, applet had no 'else' - else if (row.hasText) - { - iconOffset = av.charHeight - fm.getDescent(); - - } - else - { - iconOffset = 0; - } - - x = 0; - while (x < endRes - startRes) - { - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns( - startRes + x); - if (column > row.annotations.length - 1) - { - break; - } - } - else - { - column = startRes + x; - } - - if ((row.annotations.length <= column) - || (row.annotations[column] == null)) - { - validRes = false; - } - else - { - validRes = true; - } - - if (activeRow == i) - { - g.setColor(Color.red); - - if (av.getColumnSelection() != null) - { - for (int n = 0; n < av.getColumnSelection().size(); n++) - { - int v = av.getColumnSelection().columnAt(n); - - if (v == column) - { - g.fillRect(x * av.charWidth, y, av.charWidth, av.charHeight); - } - } - } - } - - if (av.validCharWidth - && validRes - && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter - .length() > 0)) - { - - if (centreColLabels || scaleColLabel) - { - fmWidth = (float) fm.charsWidth( - row.annotations[column].displayCharacter.toCharArray(), - 0, row.annotations[column].displayCharacter.length()); - - if (scaleColLabel) - { - // justify the label and scale to fit in column - if (fmWidth > av.charWidth) - { - // scale only if the current font isn't already small enough - fmScaling = av.charWidth; - fmScaling /= fmWidth; - // not 1.1 // g.setFont(new - // Font(ofont,AffineTransform.getScaleInstance(fmScaling, - // 1.0))); - // and update the label's width to reflect the scaling. - fmWidth = av.charWidth; - } - } - } - else - { - fmWidth = (float) fm - .charWidth(row.annotations[column].displayCharacter - .charAt(0)); - } - charOffset = (int) ((av.charWidth - fmWidth) / 2f); - - if (row.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(row.annotations[column].colour); - - if (column == 0 || row.graph > 0) - { - g.drawString(row.annotations[column].displayCharacter, - (x * av.charWidth) + charOffset, y + iconOffset + 3); // + - // 3? - } - else if (row.annotations[column - 1] == null - || (labelAllCols - || !row.annotations[column].displayCharacter - .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter - .length() < 2 && row.annotations[column].secondaryStructure == ' '))) - { - g.drawString(row.annotations[column].displayCharacter, - (x * av.charWidth) + charOffset, y + iconOffset + 3); // +3? - } - g.setFont(ofont); - } - - if (row.hasIcons) - { - if (!validRes - || (row.annotations[column].secondaryStructure != lastSS)) - { - switch (lastSS) - { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) - { - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX, 7, 8, 8); - break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (sCol == 0 - || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, - 180); - x1 += av.charWidth / 2; - } - - if (!validRes || row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - g.fillArc((x * av.charWidth) - av.charWidth, y + 4 - + iconOffset, av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - break; - - case 'E': - g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, (x * av.charWidth) - 4, - (x * av.charWidth) }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, - 3); - - break; - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - - break; - } - - if (validRes) - { - lastSS = row.annotations[column].secondaryStructure; - } - else - { - lastSS = ' '; - } - - lastSSX = (x * av.charWidth); - } - } - - column++; - x++; - } - - if (column >= row.annotations.length) - { - column = row.annotations.length - 1; - validEnd = false; - } - else - { - validEnd = true; - } - - // x ++; - - if (row.hasIcons) - { - switch (lastSS) - { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) - { - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX, 7, 8, 8); - break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (sCol == 0 || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180); - x1 += av.charWidth / 2; - } - - if (row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - g.fillArc((x * av.charWidth) - av.charWidth, - y + 4 + iconOffset, av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - - break; - - case 'E': - g.setColor(SHEET_COLOUR); - - if (!validEnd || row.annotations[endRes] == null - || row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, (x * av.charWidth) - 4, - (x * av.charWidth) }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3); - } - else - { - g.fillRect(lastSSX, y + 4 + iconOffset, x * av.charWidth - - lastSSX, 7); - } - break; - - default: - g.setColor(Color.gray); - if (!av.wrapAlignment || endRes == av.endRes) - { - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - } - - break; - } - } - - if (row.graph > 0 && row.graphHeight > 0) - { - if (row.graph == AlignmentAnnotation.LINE_GRAPH) - { - if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup]) - { - float groupmax = -999999, groupmin = 9999999; - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup != row.graphGroup) - { - continue; - } - - if (aa[gg] != row) - { - aa[gg].visible = false; - } - - if (aa[gg].graphMax > groupmax) - { - groupmax = aa[gg].graphMax; - } - if (aa[gg].graphMin < groupmin) - { - groupmin = aa[gg].graphMin; - } - } - - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup == row.graphGroup) - { - drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, - groupmax, row.graphHeight); - } - } - - graphGroupDrawn[row.graphGroup] = true; - } - else - { - drawLineGraph(g, row, startRes, endRes, y, row.graphMin, - row.graphMax, row.graphHeight); - } - } - else if (row.graph == AlignmentAnnotation.BAR_GRAPH) - { - drawBarGraph(g, row, startRes, endRes, row.graphMin, - row.graphMax, y); - } - } - - if (row.graph > 0 && row.hasText) - { - y += av.charHeight; - } - - if (row.graph == 0) - { - y += aa[i].height; - } - } - g.translate(0, +scrollOffset); - } - - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, int y, float min, float max, int graphHeight) - { - if (sRes > aa.annotations.length) - { - return; - } - - int x = 0; - - // Adjustment for fastpaint to left - if (eRes < av.endRes) - { - eRes++; - } - - eRes = Math.min(eRes, aa.annotations.length); - - int y1 = y, y2 = y; - float range = max - min; - - // //Draw origin - if (min < 0) - { - y2 = y - (int) ((0 - min / range) * graphHeight); - } - - g.setColor(Color.gray); - g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2); - - eRes = Math.min(eRes, aa.annotations.length); - - int column; - int aaMax = aa.annotations.length - 1; - - while (x < eRes - sRes) - { - column = sRes + x; - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns(column); - } - - if (column > aaMax) - { - break; - } - - if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == - // null) - { - x++; - continue; - } - - if (aa.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[column].colour); - if (column == 0 || aa.annotations[column - 1] == null) - { - y1 = y - - (int) (((aa.annotations[column].value - min) / range) * graphHeight); - } - else - { - y1 = y - - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight); - } - y2 = y - - (int) (((aa.annotations[column].value - min) / range) * graphHeight); - - g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth - + av.charWidth / 2, y2); - x++; - } - - if (aa.threshold != null) - { - g.setColor(aa.threshold.colour); - - y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight); - g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); - } + renderer.drawComponent(this, av, g, activeRow, startRes, endRes); } + + int scrollOffset = 0; - public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, float min, float max, int y) + public void setScrollOffset(int value) { - ColourSchemeI profcolour = av.getGlobalColourScheme(); - if (profcolour == null) - { - profcolour = new jalview.schemes.ZappoColourScheme(); - } - if (sRes > aa.annotations.length) - { - return; - } - Font ofont = g.getFont(); - eRes = Math.min(eRes, aa.annotations.length); - - int x = 0, y1 = y, y2 = y; - - float range = max - min; - - if (min < 0) - { - y2 = y - (int) ((0 - min / (range)) * aa.graphHeight); - } - - g.setColor(Color.gray); - - g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2); - - int column; - int aaMax = aa.annotations.length - 1; - boolean renderHistogram = true, renderProfile = false; - if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { // TODO: generalise this to have render styles for consensus/profile data - if (aa.groupRef != null) - { - renderHistogram = aa.groupRef.isShowConsensusHistogram(); - renderProfile = aa.groupRef.isShowSequenceLogo(); - } - else - { - renderHistogram = av.isShowConsensusHistogram(); - renderProfile = av.isShowSequenceLogo(); - } - } - - while (x < eRes - sRes) - { - column = sRes + x; - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns(column); - } - - if (column > aaMax) - { - break; - } - - if (aa.annotations[column] == null) - { - x++; - continue; - } - - if (aa.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[column].colour); - - y1 = y - - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - - if (renderHistogram) - { - if (y1 - y2 > 0) - { - g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); - } - else - { - g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); - } - } - // draw profile if available - if (aa.annotations[column].value != 0 && renderProfile) - { - int profl[] = getProfileFor(aa, column); - int ht = y1, htn = y2 - y1;// aa.graphHeight; - float wdth; - double ht2 = 0; - char[] dc = new char[1]; - LineMetrics lm; - for (int c = 1; profl != null && c < profl[0];) - { - dc[0] = (char) profl[c++]; - wdth = av.charWidth; - wdth /= (float) fm.charsWidth(dc, 0, 1); - - if (c > 2) - { - ht += (int) ht2; - } - { // not java 1.1 compatible: Bug # 0060064 - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) - / av.charHeight))); - lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); - g.setColor(profcolour.findColour(dc[0])); - g.drawChars(dc, 0, 1, x * av.charWidth, - (int) (ht + lm.getHeight())); - } - } - g.setFont(ofont); - } - - x++; - - } - if (aa.threshold != null) - { - g.setColor(aa.threshold.colour); - y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight); - g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); - } + scrollOffset = value; + repaint(); } - private int[] getProfileFor(AlignmentAnnotation aa, int column) + @Override + public FontMetrics getFontMetrics() { - // if (aa.autoCalculated && aa.label.startsWith("Consensus")) { - if (aa.groupRef != null && aa.groupRef.consensusData != null) - { - // && aa.groupRef.isShowSequenceLogo()) { - return AAFrequency.extractProfile(aa.groupRef.consensusData[column], - aa.groupRef.getIgnoreGapsConsensus()); - } - // TODO extend annotation row to enable dynamic and static profile data to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null) - // && av.isShowSequenceLogo()) - { - return AAFrequency.extractProfile(av.hconsensus[column], - av.getIgnoreGapsConsensus()); - } - // } - return null; + return fm; } - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, - int y, int sRes, int eRes) + @Override + public Image getFadedImage() { - eRes = Math.min(eRes, aa.annotations.length); - g.setColor(Color.white); - g.fillRect(0, 0, width, y); - g.setColor(new Color(0, 0, 180)); - - int x = 0, height; - - for (int j = sRes; j < eRes; j++) - { - if (aa.annotations[j].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[j].colour); - - height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT); - if (height > y) - { - height = y; - } - g.fillRect(x, y - height, av.charWidth, height); - x += av.charWidth; - } + return image; } - int scrollOffset = 0; - - public void setScrollOffset(int value) + @Override + public int getFadedImageWidth() { - scrollOffset = value; - repaint(); + return imgWidth; } } diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index f1d23c3..fc4fb8c 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -364,7 +364,7 @@ public class OverviewPanel extends Panel implements Runnable, lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); - ap.annotationPanel.drawGraph(mg, av.conservation, + ap.annotationPanel.renderer.drawGraph(mg, av.conservation, (int) (sampleCol) + 1, graphHeight, (int) (col * sampleCol), (int) (col * sampleCol) + 1); mg.translate(-col, -sequencesHeight); diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 5ac946a..1c6a94e 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -40,7 +40,7 @@ import java.util.*; import java.awt.*; import jalview.analysis.*; -import jalview.api.StructureSelectionManagerProvider; +import jalview.api.AlignViewportI; import jalview.bin.*; @@ -57,7 +57,7 @@ import jalview.structure.VamsasSource; * @author $author$ * @version $Revision: 1.141 $ */ -public class AlignViewport implements SelectionSource, VamsasSource +public class AlignViewport implements SelectionSource, VamsasSource, AlignViewportI { private static final int RIGHT_JUSTIFY = 1; @@ -2481,4 +2481,46 @@ public class AlignViewport implements SelectionSource, VamsasSource { normaliseSequenceLogo = state; } + + public boolean isCalcInProgress() + { + // TODO generalise to iterate over all calculators associated with av + return updatingConsensus || updatingConservation || updatingStrucConsensus; + } + + public boolean isCalculationInProgress( + AlignmentAnnotation alignmentAnnotation) + { + if (!alignmentAnnotation.autoCalculated) + return false; + if ((updatingConsensus && consensus==alignmentAnnotation) + || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation)) + || (updatingStrucConsensus && strucConsensus==alignmentAnnotation) + ) + { + return true; + } + return false; + } + + /** + * + * @return true if alignment characters should be displayed + */ + public boolean isValidCharWidth() + { + return validCharWidth; + } + + @Override + public Hashtable[] getSequenceConsensusHash() + { + return hconsensus; + } + + @Override + public Hashtable[] getRnaStructureConsensusHash() + { + return hStrucConsensus; + } } diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 2b4c0db..3c78573 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -912,7 +912,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); alabels.drawComponent((Graphics2D) pg, idWidth); pg.translate(idWidth + 3, 0); - annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1); + annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1); } return Printable.PAGE_EXISTS; diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index a611bd0..eb0189e 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -19,19 +19,16 @@ package jalview.gui; import java.awt.*; import java.awt.event.*; -import java.awt.font.LineMetrics; -import java.awt.geom.AffineTransform; import java.awt.image.*; import java.util.Hashtable; import javax.swing.*; -import com.stevesoft.pat.Regex; - import jalview.analysis.AAFrequency; import jalview.analysis.StructureFrequency; import jalview.datamodel.*; -import jalview.schemes.ColourSchemeI; +import jalview.renderer.AnnotationRenderer; +import jalview.renderer.AwtRenderPanelI; /** * DOCUMENT ME! @@ -39,8 +36,9 @@ import jalview.schemes.ColourSchemeI; * @author $author$ * @version $Revision$ */ -public class AnnotationPanel extends JPanel implements MouseListener, - MouseMotionListener, ActionListener, AdjustmentListener +public class AnnotationPanel extends JPanel implements AwtRenderPanelI, + MouseListener, MouseMotionListener, ActionListener, + AdjustmentListener { final String HELIX = "Helix"; @@ -57,28 +55,28 @@ public class AnnotationPanel extends JPanel implements MouseListener, final String COLOUR = "Colour"; - final Color HELIX_COLOUR = Color.red.darker(); + public final Color HELIX_COLOUR = Color.red.darker(); - final Color SHEET_COLOUR = Color.green.darker().darker(); + public final Color SHEET_COLOUR = Color.green.darker().darker(); - final Color STEM_COLOUR = Color.blue.darker(); + public final Color STEM_COLOUR = Color.blue.darker(); /** DOCUMENT ME!! */ - AlignViewport av; + public AlignViewport av; AlignmentPanel ap; - int activeRow = -1; + public int activeRow = -1; - BufferedImage image; + public BufferedImage image; - BufferedImage fadedImage; + public BufferedImage fadedImage; Graphics2D gg; - FontMetrics fm; + public FontMetrics fm; - int imgWidth = 0; + public int imgWidth = 0; boolean fastPaint = false; @@ -100,6 +98,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, int cursorY = 0; + public final AnnotationRenderer renderer; + /** * Creates a new AnnotationPanel object. * @@ -121,11 +121,13 @@ public class AnnotationPanel extends JPanel implements MouseListener, addMouseMotionListener(this); ap.annotationScroller.getVerticalScrollBar() .addAdjustmentListener(this); + renderer = new AnnotationRenderer(); } public AnnotationPanel(AlignViewport av) { this.av = av; + renderer = new AnnotationRenderer(); } /** @@ -863,865 +865,24 @@ public class AnnotationPanel extends JPanel implements MouseListener, return; } - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - - int x = 0, y = 0; - int column = 0; - char lastSS; - int lastSSX; - int iconOffset = 0; - boolean validRes = false; - boolean validEnd = false; - boolean labelAllCols = false; - boolean centreColLabels, centreColLabelsDef = av - .getCentreColumnLabels(); - boolean scaleColLabel = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; - int charOffset = 0; // offset for a label - float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a - // column. - Font ofont = g.getFont(); - // \u03B2 \u03B1 - for (int i = 0; i < aa.length; i++) - { - AlignmentAnnotation row = aa[i]; - - if (!row.visible) - { - continue; - } - centreColLabels = row.centreColLabels || centreColLabelsDef; - labelAllCols = row.showAllColLabels; - scaleColLabel = row.scaleColLabel; - lastSS = ' '; - lastSSX = 0; - if (row.graph > 0) - { - if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) - { - continue; - } - - // this is so that we draw the characters below the graph - y += row.height; - - if (row.hasText) - { - iconOffset = av.charHeight - fm.getDescent(); - y -= av.charHeight; - } - } - else if (row.hasText) - { - iconOffset = av.charHeight - fm.getDescent(); - - } - else - { - iconOffset = 0; - } - - if (av.updatingConsensus && aa[i] == av.consensus) - { - y += av.charHeight; - - g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - - row.height, imgWidth, y, this); - g.setColor(Color.black); - // g.drawString("Calculating Consensus....",20, y-row.height/2); - - continue; - } - else if (av.updatingConservation - && aa[i].label.equals("Conservation")) - { - - y += av.charHeight; - g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - - row.height, imgWidth, y, this); - - g.setColor(Color.black); - // g.drawString("Calculating Conservation.....",20, y-row.height/2); - - continue; - } - else if (av.updatingConservation && aa[i].label.equals("Quality")) - { - - y += av.charHeight; - g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - - row.height, imgWidth, y, this); - g.setColor(Color.black); - // / g.drawString("Calculating Quality....",20, y-row.height/2); - - continue; - } - - // first pass sets up state for drawing continuation from left-hand column - // of startRes - x = (startRes == 0) ? 0 : -1; - while (x < endRes - startRes) - { - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns( - startRes + x); - if (column > row.annotations.length - 1) - { - break; - } - } - else - { - column = startRes + x; - } - - if ((row.annotations == null) || (row.annotations.length <= column) - || (row.annotations[column] == null)) - { - validRes = false; - } - else - { - validRes = true; - } - if (x > -1) - { - if (activeRow == i) - { - g.setColor(Color.red); - - if (av.getColumnSelection() != null) - { - for (int n = 0; n < av.getColumnSelection().size(); n++) - { - int v = av.getColumnSelection().columnAt(n); - - if (v == column) - { - g.fillRect(x * av.charWidth, y, av.charWidth, - av.charHeight); - } - } - } - } - - if (av.validCharWidth - && validRes - && row.annotations[column].displayCharacter != null - && (row.annotations[column].displayCharacter.length() > 0)) - { - - if (centreColLabels || scaleColLabel) - { - fmWidth = (float) fm.charsWidth( - row.annotations[column].displayCharacter - .toCharArray(), 0, - row.annotations[column].displayCharacter.length()); - - if (scaleColLabel) - { - // justify the label and scale to fit in column - if (fmWidth > av.charWidth) - { - // scale only if the current font isn't already small enough - fmScaling = av.charWidth; - fmScaling /= fmWidth; - g.setFont(ofont.deriveFont(AffineTransform - .getScaleInstance(fmScaling, 1.0))); - // and update the label's width to reflect the scaling. - fmWidth = av.charWidth; - } - } - } - else - { - fmWidth = (float) fm - .charWidth(row.annotations[column].displayCharacter - .charAt(0)); - } - charOffset = (int) ((av.charWidth - fmWidth) / 2f); - - if (row.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(row.annotations[column].colour); - - if (column == 0 || row.graph > 0) - { - g.drawString(row.annotations[column].displayCharacter, - (x * av.charWidth) + charOffset, y + iconOffset); - } - else if (row.annotations[column - 1] == null - || (labelAllCols - || !row.annotations[column].displayCharacter - .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter - .length() < 2 && row.annotations[column].secondaryStructure == ' '))) - { - g.drawString(row.annotations[column].displayCharacter, x - * av.charWidth + charOffset, y + iconOffset); - } - g.setFont(ofont); - } - } - if (row.hasIcons) - { - char ss = validRes ? row.annotations[column].secondaryStructure - : ' '; - if (ss == 'S') - { - // distinguish between forward/backward base-pairing - if (row.annotations[column].displayCharacter.indexOf(')') > -1) - { - ss = 's'; - } - } - if (!validRes || (ss != lastSS)) - { - if (x > -1) - { - switch (lastSS) - { - case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - case 'S': // Stem case for RNA secondary structure - case 's': // and opposite direction - drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - - break; - } - } - if (validRes) - { - lastSS = ss; - } - else - { - lastSS = ' '; - } - if (x > -1) - { - lastSSX = (x * av.charWidth); - } - } - } - column++; - x++; - } - if (column >= row.annotations.length) - { - column = row.annotations.length - 1; - validEnd = false; - } - else - { - validEnd = true; - } - - // x ++; - - if (row.hasIcons) - { - switch (lastSS) - { - case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - case 's': - case 'S': // Stem case for RNA secondary structure - drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - default: - drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - } - } - - if (row.graph > 0 && row.graphHeight > 0) - { - if (row.graph == AlignmentAnnotation.LINE_GRAPH) - { - if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup]) - { - float groupmax = -999999, groupmin = 9999999; - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup != row.graphGroup) - { - continue; - } - - if (aa[gg] != row) - { - aa[gg].visible = false; - } - - if (aa[gg].graphMax > groupmax) - { - groupmax = aa[gg].graphMax; - } - if (aa[gg].graphMin < groupmin) - { - groupmin = aa[gg].graphMin; - } - } - - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup == row.graphGroup) - { - drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, - groupmax, row.graphHeight); - } - } - - graphGroupDrawn[row.graphGroup] = true; - } - else - { - drawLineGraph(g, row, startRes, endRes, y, row.graphMin, - row.graphMax, row.graphHeight); - } - } - else if (row.graph == AlignmentAnnotation.BAR_GRAPH) - { - drawBarGraph(g, row, startRes, endRes, row.graphMin, - row.graphMax, y); - } - } - - if (row.graph > 0 && row.hasText) - { - y += av.charHeight; - } - - if (row.graph == 0) - { - y += aa[i].height; - } - } + renderer.drawComponent(this, av, g, activeRow, startRes, endRes); } - private void drawStemAnnot(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) + @Override + public FontMetrics getFontMetrics() { - g.setColor(STEM_COLOUR); - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - Regex closeparen = new Regex("(\\))"); - - String dc = column == 0 ? "" - : row.annotations[column - 1].displayCharacter; - - boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null - || !dc.equals(row.annotations[sCol - 1].displayCharacter); - boolean diffdownstream = !validRes || !validEnd - || row.annotations[column] == null - || !dc.equals(row.annotations[column].displayCharacter); - // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); - // If a closing base pair half of the stem, display a backward arrow - if (column > 0 && closeparen.search(dc)) - { - if (diffupstream) - // if (validRes && column>1 && row.annotations[column-2]!=null && - // dc.equals(row.annotations[column-2].displayCharacter)) - { - g.fillPolygon(new int[] - { lastSSX + 5, lastSSX + 5, lastSSX }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); - x1 += 5; - } - if (diffdownstream) - { - x2 -= 1; - } - } - else - { - // display a forward arrow - if (diffdownstream) - { - g.fillPolygon(new int[] - { x2 - 5, x2 - 5, x2 }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); - x2 -= 5; - } - if (diffupstream) - { - x1 += 1; - } - } - // draw arrow body - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); + return fm; } - private void drawGlyphLine(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) + @Override + public Image getFadedImage() { - g.setColor(Color.gray); - g - .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); + return fadedImage; } - private void drawSheetAnnot(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) + @Override + public int getFadedImageWidth() { - g.setColor(SHEET_COLOUR); - - if (!validEnd || !validRes || row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'E') - { - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - lastSSX - - 4, 7); - g.fillPolygon( - new int[] - { (x * av.charWidth) - 4, (x * av.charWidth) - 4, - (x * av.charWidth) }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, - 3); - } - else - { - g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth - - lastSSX, 7); - } - + return imgWidth; } - - private void drawHelixAnnot(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) - { - g.setColor(HELIX_COLOUR); - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (MAC) - { - int ofs = av.charWidth / 2; - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8); - if (sCol == 0 || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - } - else - { - // g.setColor(Color.orange); - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, - 0, 0); - } - if (!validRes || row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - - } - else - { - // g.setColor(Color.magenta); - g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs - + 1, 8, 0, 0); - - } - - return; - } - - if (sCol == 0 || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180); - x1 += av.charWidth / 2; - } - - if (!validRes || row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - g.fillArc((x * av.charWidth) - av.charWidth, y + 4 + iconOffset, - av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - } - - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, int y, float min, float max, int graphHeight) - { - if (sRes > aa.annotations.length) - { - return; - } - - int x = 0; - - // Adjustment for fastpaint to left - if (eRes < av.endRes) - { - eRes++; - } - - eRes = Math.min(eRes, aa.annotations.length); - - if (sRes == 0) - { - x++; - } - - int y1 = y, y2 = y; - float range = max - min; - - // //Draw origin - if (min < 0) - { - y2 = y - (int) ((0 - min / range) * graphHeight); - } - - g.setColor(Color.gray); - g.drawLine(x - av.charWidth, y2, (eRes - sRes + 1) * av.charWidth, y2); - - eRes = Math.min(eRes, aa.annotations.length); - - int column; - int aaMax = aa.annotations.length - 1; - - while (x < eRes - sRes) - { - column = sRes + x; - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns(column); - } - - if (column > aaMax) - { - break; - } - - if (aa.annotations[column] == null - || aa.annotations[column - 1] == null) - { - x++; - continue; - } - - if (aa.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[column].colour); - - y1 = y - - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight); - y2 = y - - (int) (((aa.annotations[column].value - min) / range) * graphHeight); - - g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth - + av.charWidth / 2, y2); - x++; - } - - if (aa.threshold != null) - { - g.setColor(aa.threshold.colour); - Graphics2D g2 = (Graphics2D) g; - g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - - y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight); - g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); - g2.setStroke(new BasicStroke()); - } - } - - public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, float min, float max, int y) - { - ColourSchemeI profcolour = av.getGlobalColourScheme(); - if (profcolour == null) - { - profcolour = new jalview.schemes.ZappoColourScheme(); - } - if (sRes > aa.annotations.length) - { - return; - } - Font ofont = g.getFont(); - eRes = Math.min(eRes, aa.annotations.length); - - int x = 0, y1 = y, y2 = y; - - float range = max - min; - - if (min < 0) - { - y2 = y - (int) ((0 - min / (range)) * aa.graphHeight); - } - - g.setColor(Color.gray); - - g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2); - - int column; - int aaMax = aa.annotations.length - 1; - boolean renderHistogram = true, renderProfile = true, normaliseProfile=false; -// if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { - // TODO: generalise this to have render styles for consensus/profile data - if (aa.groupRef != null) - { - renderHistogram = aa.groupRef.isShowConsensusHistogram(); - renderProfile = aa.groupRef.isShowSequenceLogo(); - normaliseProfile= aa.groupRef.isNormaliseSequenceLogo(); - } - else - { - renderHistogram = av.isShowConsensusHistogram(); - renderProfile = av.isShowSequenceLogo(); - normaliseProfile= av.isNormaliseSequenceLogo(); - } - } - while (x < eRes - sRes) - { - column = sRes + x; - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns(column); - } - - if (column > aaMax) - { - break; - } - - if (aa.annotations[column] == null) - { - x++; - continue; - } - if (aa.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[column].colour); - - y1 = y - - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - - if (renderHistogram) - { - if (y1 - y2 > 0) - { - g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); - } - else - { - g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); - } - } - // draw profile if available - if (renderProfile && aa.annotations[column].value != 0) - { - - int profl[] = getProfileFor(aa, column); - // just try to draw the logo if profl is not null - if (profl != null) - { - - float ht = normaliseProfile ? y-aa.graphHeight : y1; - double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight; - float wdth; - double ht2 = 0; - char[] dc; - - /** - * profl.length == 52 indicates that the profile of a secondary - * structure conservation row was accesed. - * Therefore dc gets length 2, to have space for a basepair instead of - * just a single nucleotide - */ - if (profl.length == 52) - { - dc = new char[2]; - } - else - { - dc = new char[1]; - } - LineMetrics lm=g.getFontMetrics(ofont).getLineMetrics("Q", g); - double scale = 1f/(normaliseProfile ? profl[1] : 100f); - float ofontHeight = 1f/lm.getAscent();// magnify to fill box - double scl=0.0; - for (int c = 2; profl != null && c < profl[0];) - { - dc[0] = (char) profl[c++]; - - if (aa.label.startsWith("StrucConsensus")) - { - dc[1] = (char) profl[c++]; - } - - wdth = av.charWidth; - wdth /= (float) fm.charsWidth(dc, 0, dc.length); - - ht += scl; - { - // if (aa.annotations[column].value==0) { - // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, - // (ht2=(aa.graphHeight*0.1/av.charHeight))))); - // ht = y2-(int)ht2; - // } else { - scl=((double)htn)*scale* ((double) profl[c++]); - lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics().getFontRenderContext()); - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, scl/lm.getAscent()))); - lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); - - // htn -=ht2; - // } - // ? );// try to get a - // colourscheme for the - // group(aa.groupRef.cs==null) - // ? av.textColour2 : - // cs.findColour(dc)); - // System.out.println(dc[0]); - // Debug - render boxes around characters - // g.setColor(Color.red); - // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, (int)(scl)); - // g.setColor(profcolour.findColour(dc[0]).darker()); - g.setColor(profcolour.findColour(dc[0])); - // (av.globalColourScheme!=null) - g.drawChars(dc, 0, dc.length, x * av.charWidth, - (int) (ht + (scl-lm.getDescent()-lm.getBaselineOffsets()[lm.getBaselineIndex()]))); - // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); - } - } - g.setFont(ofont); - } - } - x++; - } - if (aa.threshold != null) - { - g.setColor(aa.threshold.colour); - Graphics2D g2 = (Graphics2D) g; - g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - - y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight); - g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); - g2.setStroke(new BasicStroke()); - } - } - - private int[] getProfileFor(AlignmentAnnotation aa, int column) - { - if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { - if (aa.groupRef != null && aa.groupRef.consensusData != null - && aa.groupRef.isShowSequenceLogo()) - { - return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], aa.groupRef - .getIgnoreGapsConsensus()); - } - // TODO extend annotation row to enable dynamic and static profile data to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null - && av.isShowSequenceLogo()) - { - return AAFrequency.extractProfile(av.hconsensus[column], av - .getIgnoreGapsConsensus()); - } - } - else - { - if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) - { - if (aa.groupRef != null && aa.groupRef.consensusData != null - && aa.groupRef.isShowSequenceLogo()) - { - //TODO check what happens for group selections - return StructureFrequency.extractProfile( - aa.groupRef.consensusData[column], aa.groupRef - .getIgnoreGapsConsensus()); - } - // TODO extend annotation row to enable dynamic and static profile data - // to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null - && av.isShowSequenceLogo()) - { - return StructureFrequency.extractProfile(av.hStrucConsensus[column], - av.getIgnoreGapsConsensus()); - } - } - } - return null; - } - - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, - int y, int sRes, int eRes) - { - eRes = Math.min(eRes, aa.annotations.length); - g.setColor(Color.white); - g.fillRect(0, 0, width, y); - g.setColor(new Color(0, 0, 180)); - - int x = 0, height; - - for (int j = sRes; j < eRes; j++) - { - if (aa.annotations[j] != null) - { - if (aa.annotations[j].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[j].colour); - - height = (int) ((aa.annotations[j].value / aa.graphMax) * y); - if (height > y) - { - height = y; - } - - g.fillRect(x, y - height, av.charWidth, height); - } - x += av.charWidth; - } - } - } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 8067808..7e00f2e 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -17,6 +17,8 @@ */ package jalview.gui; +import jalview.renderer.AnnotationRenderer; + import java.awt.*; import java.awt.event.*; import java.awt.image.*; @@ -36,6 +38,7 @@ public class OverviewPanel extends JPanel implements Runnable AlignmentPanel ap; + final AnnotationRenderer renderer = new AnnotationRenderer(); float scalew = 1f; float scaleh = 1f; @@ -356,12 +359,13 @@ public class OverviewPanel extends JPanel implements Runnable if (av.conservation != 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.conservation, (int) (sampleCol) + 1, graphHeight, (int) (col * sampleCol), (int) (col * sampleCol) + 1); mg.translate(-col, -sequencesHeight); diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index fb5367f..9e3f8a2 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -572,7 +572,7 @@ 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); -- 1.7.10.2