From 3fca8f1a5cebad8b73747d121622d1f63a5f9178 Mon Sep 17 00:00:00 2001 From: kiramt Date: Fri, 24 Mar 2017 11:36:35 +0000 Subject: [PATCH] JAL-2388 Removing AlignmentPanel dependency (mostly) --- src/jalview/appletgui/OverviewCanvas.java | 12 +++++------- src/jalview/appletgui/OverviewPanel.java | 8 ++------ src/jalview/gui/OverviewCanvas.java | 20 ++++++++------------ src/jalview/gui/OverviewPanel.java | 5 +++-- src/jalview/gui/SequenceRenderer.java | 7 ++++--- 5 files changed, 22 insertions(+), 30 deletions(-) diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java index dea8ddc..51819cd 100644 --- a/src/jalview/appletgui/OverviewCanvas.java +++ b/src/jalview/appletgui/OverviewCanvas.java @@ -48,8 +48,6 @@ public class OverviewCanvas extends JComponent private AlignViewport av; - private AlignmentPanel ap; - // Can set different properties in this seqCanvas than // main visible SeqCanvas private SequenceRenderer sr; @@ -59,11 +57,10 @@ public class OverviewCanvas extends JComponent private Frame nullFrame; public OverviewCanvas(OverviewDimensions overviewDims, - AlignViewport alignvp, AlignmentPanel alignp) + AlignViewport alignvp) { od = overviewDims; - av = alignp.av; - ap = alignp; + av = alignvp; nullFrame = new Frame(); nullFrame.addNotify(); @@ -95,7 +92,8 @@ public class OverviewCanvas extends JComponent } } - public void draw(boolean showSequenceFeatures, boolean showAnnotation) + public void draw(boolean showSequenceFeatures, boolean showAnnotation, + AlignmentPanel ap) { miniMe = null; @@ -137,7 +135,7 @@ public class OverviewCanvas extends JComponent if (restart) { restart = false; - draw(showSequenceFeatures, showAnnotation); + draw(showSequenceFeatures, showAnnotation, ap); } else { diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 8962bdc..d64c72f 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -53,7 +53,7 @@ public class OverviewPanel extends Panel implements Runnable, od = new OverviewDimensions(av.getRanges(), (av.isShowAnnotation() && av.getSequenceConsensusHash() != null)); - oviewCanvas = new OverviewCanvas(od, av, ap); + oviewCanvas = new OverviewCanvas(od, av); setLayout(new BorderLayout()); add(oviewCanvas, BorderLayout.CENTER); @@ -157,7 +157,7 @@ public class OverviewPanel extends Panel implements Runnable, { oviewCanvas.draw(av.isShowSequenceFeatures(), (av.isShowAnnotation() && av - .getAlignmentConservationAnnotation() != null)); + .getAlignmentConservationAnnotation() != null), ap); setBoxPosition(); } @@ -172,8 +172,4 @@ public class OverviewPanel extends Panel implements Runnable, .getHiddenSequences(), av.getColumnSelection(), av.getRanges()); repaint(); } - - - - } diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java index 8c02423..3ced9ee 100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@ -48,8 +48,6 @@ public class OverviewCanvas extends JComponent private BufferedImage lastMiniMe = null; - - // Can set different properties in this seqCanvas than // main visible SeqCanvas private SequenceRenderer sr; @@ -60,21 +58,18 @@ public class OverviewCanvas extends JComponent OverviewDimensions od; - AlignViewport av; - - AlignmentPanel ap; + AlignViewportI av; public OverviewCanvas(OverviewDimensions overviewDims, - AlignViewportI alignvp, AlignmentPanel alignp) + AlignViewportI alignvp) { od = overviewDims; - av = alignp.av; - ap = alignp; + av = alignvp; sr = new SequenceRenderer(av); sr.renderGaps = false; sr.forOverview = true; - fr = new FeatureRenderer(ap); + fr = new jalview.renderer.seqfeatures.FeatureRenderer(av); } /* @@ -97,13 +92,14 @@ public class OverviewCanvas extends JComponent } } - public void draw(boolean showSequenceFeatures, boolean showAnnotation) + public void draw(boolean showSequenceFeatures, boolean showAnnotation, + FeatureRenderer transferRenderer) { miniMe = null; if (showSequenceFeatures) { - fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); + fr.transferSettings(transferRenderer); } // why do we need to set preferred size again? was set in @@ -152,7 +148,7 @@ public class OverviewCanvas extends JComponent if (restart) { restart = false; - draw(showSequenceFeatures, showAnnotation); + draw(showSequenceFeatures, showAnnotation, transferRenderer); } else { diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index faa94e9..68b4dc5 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -64,7 +64,7 @@ public class OverviewPanel extends JPanel implements Runnable (av.isShowAnnotation() && av .getAlignmentConservationAnnotation() != null)); - oviewCanvas = new OverviewCanvas(od, av, ap); + oviewCanvas = new OverviewCanvas(od, av); setLayout(new BorderLayout()); add(oviewCanvas, BorderLayout.CENTER); @@ -143,7 +143,8 @@ public class OverviewPanel extends JPanel implements Runnable { oviewCanvas.draw(av.isShowSequenceFeatures(), (av.isShowAnnotation() && av - .getAlignmentConservationAnnotation() != null)); + .getAlignmentConservationAnnotation() != null), ap + .getSeqPanel().seqCanvas.getFeatureRenderer()); setBoxPosition(); } diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 1c0420d..2a2a0cf 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.AlignViewportI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.renderer.ResidueShaderI; @@ -34,7 +35,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { final static int CHAR_TO_UPPER = 'A' - 'a'; - AlignViewport av; + AlignViewportI av; FontMetrics fm; @@ -57,7 +58,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer * * @param viewport */ - public SequenceRenderer(AlignViewport viewport) + public SequenceRenderer(AlignViewportI viewport) { this.av = viewport; } @@ -181,7 +182,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer drawBoxes(seq, start, end, y1); - if (av.validCharWidth) + if (av.isValidCharWidth()) { drawText(seq, start, end, y1); } -- 1.7.10.2