From 14855b5ae4adcfeaa1fa9a61fea11b20a7452260 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 5 Nov 2018 14:47:03 +0000 Subject: [PATCH] JAL-3148 SequenceRenderer interface renamed SequenceRendererI --- src/jalview/appletgui/SequenceRenderer.java | 2 +- src/jalview/ext/jmol/JmolCommands.java | 7 +++---- src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 6 +++--- src/jalview/ext/varna/VarnaCommands.java | 4 ++-- src/jalview/javascript/MouseOverStructureListener.java | 4 ++-- 5 files changed, 11 insertions(+), 12 deletions(-) diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index e55f2a5..907d29e 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -30,7 +30,7 @@ import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; -public class SequenceRenderer implements jalview.api.SequenceRenderer +public class SequenceRenderer implements jalview.api.SequenceRendererI { final static int CHAR_TO_UPPER = 'A' - 'a'; diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java index 8fb0de6..b2aeee4 100644 --- a/src/jalview/ext/jmol/JmolCommands.java +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -23,7 +23,7 @@ package jalview.ext.jmol; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; +import jalview.api.SequenceRendererI; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; @@ -55,7 +55,7 @@ public class JmolCommands */ public static StructureMappingcommandSet[] getColourBySequenceCommand( StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, + SequenceI[][] sequence, SequenceRendererI sr, AlignmentViewPanel viewPanel) { FeatureRenderer fr = viewPanel.getFeatureRenderer(); @@ -69,8 +69,7 @@ public class JmolCommands { StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); StringBuffer command = new StringBuffer(); - StructureMappingcommandSet smc; - ArrayList str = new ArrayList(); + List str = new ArrayList<>(); if (mapping == null || mapping.length < 1) { diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index dad8511..f952bff 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -23,7 +23,7 @@ package jalview.ext.rbvi.chimera; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; +import jalview.api.SequenceRendererI; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceFeature; @@ -66,7 +66,7 @@ public class ChimeraCommands */ public static StructureMappingcommandSet[] getColourBySequenceCommand( StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, + SequenceI[][] sequence, SequenceRendererI sr, AlignmentViewPanel viewPanel) { Map colourMap = buildColoursMap(ssm, files, @@ -188,7 +188,7 @@ public class ChimeraCommands */ protected static Map buildColoursMap( StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, + SequenceI[][] sequence, SequenceRendererI sr, AlignmentViewPanel viewPanel) { FeatureRenderer fr = viewPanel.getFeatureRenderer(); diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java index 4dd0648..e0524e8 100644 --- a/src/jalview/ext/varna/VarnaCommands.java +++ b/src/jalview/ext/varna/VarnaCommands.java @@ -20,7 +20,7 @@ */ package jalview.ext.varna; -import jalview.api.SequenceRenderer; +import jalview.api.SequenceRendererI; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.renderer.seqfeatures.FeatureColourFinder; @@ -47,7 +47,7 @@ public class VarnaCommands */ public static String[] getColourBySequenceCommand( StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, + SequenceI[][] sequence, SequenceRendererI sr, FeatureColourFinder finder, AlignmentI alignment) { ArrayList str = new ArrayList(); diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java index 6071933..fd2a4d5 100644 --- a/src/jalview/javascript/MouseOverStructureListener.java +++ b/src/jalview/javascript/MouseOverStructureListener.java @@ -22,7 +22,7 @@ package jalview.javascript; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; +import jalview.api.SequenceRendererI; import jalview.appletgui.AlignFrame; import jalview.bin.JalviewLite; import jalview.datamodel.SequenceI; @@ -203,7 +203,7 @@ public class MouseOverStructureListener extends JSFunctionExec // } } - SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source) + SequenceRendererI sr = ((jalview.appletgui.AlignmentPanel) source) .getSequenceRenderer(); FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av .isShowSequenceFeatures() -- 1.7.10.2