X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=b61f1cb6eb6be4f9e07a2e93cde6a442189139f7;hb=298c2b85845dbaabda7e3304751cc856e7b0ad30;hp=d4fcf979ac994dbae1117357d34420d2e11c134a;hpb=bbfdb203ce3a889600caa52478478b75ab03809f;p=jalview.git 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; } }