X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=09152d69662e720be130742507c141dea6f4fdd3;hb=d1d2ea58719115718d0672a9f8fb85c48a908468;hp=ab27d8a60692b3fef7cae034f9528a2fb330b01e;hpb=ca03475c238445cb80495c117fee9e508d5f6985;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index ab27d8a..09152d6 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -35,16 +35,29 @@ import java.awt.Image; import java.awt.font.LineMetrics; import java.awt.geom.AffineTransform; import java.awt.image.ImageObserver; +import java.util.BitSet; import java.util.Hashtable; import com.stevesoft.pat.Regex; public class AnnotationRenderer { + /** + * flag indicating if timing and redraw parameter info should be output + */ + private final boolean debugRedraw; public AnnotationRenderer() { - // TODO Auto-generated constructor stub + this(false); + } + /** + * Create a new annotation Renderer + * @param debugRedraw flag indicating if timing and redraw parameter info should be output + */ + public AnnotationRenderer(boolean debugRedraw) + { + this.debugRedraw=debugRedraw; } public void drawStemAnnot(Graphics g, Annotation[] row_annotations, @@ -141,7 +154,23 @@ public class AnnotationRenderer * width of image to render in panel */ private int imgWidth; - + /** + * offset to beginning of visible area + */ + private int sOffset; + /** + * offset to end of visible area + */ + private int visHeight; + /** + * indicate if the renderer should only render the visible portion of the annotation given the current view settings + */ + private boolean useClip=true; + /** + * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1 + */ + private boolean canClip=false; + // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI // av) public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel, @@ -151,6 +180,22 @@ public class AnnotationRenderer annotationPanel = annotPanel; fadedImage = annotPanel.getFadedImage(); imgWidth = annotPanel.getFadedImageWidth(); + // visible area for rendering + int[] bounds=annotPanel.getVisibleVRange(); + if (bounds!=null) + { + sOffset = bounds[0]; + visHeight = bounds[1]; + if (visHeight==0) + { + useClip=false; + } else { + useClip=canClip; + } + } else { + useClip=false; + } + updateFromAlignViewport(av); } @@ -195,7 +240,7 @@ public class AnnotationRenderer } // TODO extend annotation row to enable dynamic and static profile data to // be stored - if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile) + if (aa.groupRef == null && aa.sequenceRef == null) { return AAFrequency.extractProfile(hconsensus[column], av_ignoreGapsConsensus); @@ -217,7 +262,7 @@ public class AnnotationRenderer // to // be stored if (aa.groupRef == null && aa.sequenceRef == null - && av_renderProfile && hStrucConsensus != null + && hStrucConsensus != null && hStrucConsensus.length > column) { return StructureFrequency.extractProfile(hStrucConsensus[column], @@ -250,6 +295,7 @@ public class AnnotationRenderer AlignViewportI av, Graphics g, int activeRow, int startRes, int endRes) { + long stime=System.currentTimeMillis(); boolean usedFaded = false; // NOTES: // AnnotationPanel needs to implement: ImageObserver, access to @@ -272,15 +318,41 @@ public class AnnotationRenderer boolean centreColLabels, centreColLabelsDef = av .getCentreColumnLabels(); boolean scaleColLabel = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; + AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation(); + boolean renderHistogram = true, renderProfile = true, normaliseProfile = false; + + BitSet graphGroupDrawn = new BitSet(); 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 + // debug ints + int yfrom=0,f_i=0,yto=0,f_to=0; + boolean clipst=false,clipend=false; for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; + { + // check if this is a consensus annotation row and set the display settings appropriately + // TODO: generalise this to have render styles for consensus/profile + // data + if (row.groupRef != null && row == row.groupRef.getConsensus()) + { + renderHistogram = row.groupRef.isShowConsensusHistogram(); + renderProfile = row.groupRef.isShowSequenceLogo(); + normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); + } + else if (row == consensusAnnot || row == structConsensusAnnot) + { + renderHistogram = av_renderHistogram; + renderProfile = av_renderProfile; + normaliseProfile = av_normaliseProfile; + } else { + renderHistogram = true; + // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer + } + } Annotation[] row_annotations = row.annotations; if (!row.visible) { @@ -291,10 +363,20 @@ public class AnnotationRenderer scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; + + if (!useClip || ((y-charHeight)=sOffset)) + {// if_in_visible_region + if (!clipst) + { + clipst=true; + yfrom=y; + f_i=i; + } + yto = y; + f_to=i; if (row.graph > 0) { - if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) - { + if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) { continue; } @@ -569,8 +651,9 @@ public class AnnotationRenderer { if (row.graph == AlignmentAnnotation.LINE_GRAPH) { - if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup]) + if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup)) { + // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels float groupmax = -999999, groupmin = 9999999; for (int gg = 0; gg < aa.length; gg++) { @@ -602,7 +685,7 @@ public class AnnotationRenderer } } - graphGroupDrawn[row.graphGroup] = true; + graphGroupDrawn.set(row.graphGroup); } else { @@ -613,10 +696,15 @@ public class AnnotationRenderer else if (row.graph == AlignmentAnnotation.BAR_GRAPH) { drawBarGraph(g, row, row_annotations, startRes, endRes, - row.graphMin, row.graphMax, y); + row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile); } } - + } else { + if (clipst && !clipend) + { + clipend = true; + } + }// end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; @@ -627,6 +715,27 @@ public class AnnotationRenderer y += aa[i].height; } } + if (debugRedraw) + { + if (canClip) + { + if (clipst) + { + System.err.println("Start clip at : " + yfrom + " (index " + f_i + + ")"); + } + if (clipend) + { + System.err.println("End clip at : " + yto + " (index " + f_to + + ")"); + } + } + ; + System.err.println("Annotation Rendering time:" + + (System.currentTimeMillis() - stime)); + } + ; + return !usedFaded; } @@ -823,7 +932,7 @@ public class AnnotationRenderer public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, int eRes, float min, - float max, int y) + float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile) { if (sRes > aa_annotations.length) { @@ -847,23 +956,6 @@ public class AnnotationRenderer 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_renderHistogram; - renderProfile = av_renderProfile; - normaliseProfile = av_normaliseProfile; - } - } while (x < eRes - sRes) { column = sRes + x;