From: Renia Correya <rcorreya001@dundee.ac.uk>
Date: Wed, 3 Jul 2024 09:49:27 +0000 (+0100)
Subject: JAL-4392 Code Refactoring
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9660ad220459678b9361983921c7d65cb8d21c99;p=jalview.git

JAL-4392 Code Refactoring

Removed the usage of Message.properties in non UI classes
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 3ca5bcb..0284498 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -3082,7 +3082,7 @@ public class AlignmentUtils
       if (aa != null)
       {
 
-        if (ssSource.equals(MessageManager.getString("option.ss_providers_all")))
+        if (ssSource.equals(Constants.SS_ALL_PROVIDERS))
         {
           ssAnnots.addAll(Arrays.asList(aa));
           continue;
@@ -3133,7 +3133,7 @@ public class AlignmentUtils
         if (label.equals(aa.label))
         {
 
-          if (selectedSSSource.equals(MessageManager.getString("option.ss_providers_all")))
+          if (selectedSSSource.equals(Constants.SS_ALL_PROVIDERS))
           {
             ssAlignmentAnnotationForSequences
                     .computeIfAbsent(aa.sequenceRef.getDatasetSequence(),
diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
index 4e3a3de..d7859f1 100644
--- a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
@@ -31,6 +31,7 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceI;
 import jalview.math.Matrix;
 import jalview.math.MatrixI;
+import jalview.util.Constants;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
@@ -114,7 +115,7 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel
     //secondary structure source parameter selected by the user from the drop down.
     String ssSource = params.getSecondaryStructureSource(); 
     if(ssSource == null || ssSource == "") {
-      ssSource = MessageManager.getString("option.ss_providers_all");
+      ssSource = Constants.SS_ALL_PROVIDERS;
     }
     ssRateMatrix = ScoreModels.getInstance().getSecondaryStructureMatrix();
         
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 75d4460..29e18a6 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -37,6 +37,7 @@ import jalview.analysis.Conservation;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.util.Constants;
 import jalview.util.MessageManager;
 
 /**
@@ -635,7 +636,7 @@ public class SequenceGroup implements AnnotatedCollectionI
         ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa.getAlignmentAnnotation());
       }
       if(ssSources != null) {
-        ssSources.add(MessageManager.getString("option.ss_providers_all"));
+        ssSources.add(Constants.SS_ALL_PROVIDERS);
 
         for(String ssSource : ssSources) {
           ProfilesI hSSConsensus = AAFrequency.calculateSS(sequences, startRes,  endRes + 1, showSequenceLogo,
diff --git a/src/jalview/util/Constants.java b/src/jalview/util/Constants.java
index f8e4e4f..59f88ae 100644
--- a/src/jalview/util/Constants.java
+++ b/src/jalview/util/Constants.java
@@ -47,5 +47,9 @@ public class Constants
       // Add other secondary structure labels here if needed
   } 
   
-  public static final String SS_PROVIDER_PROPERTY = "SS_PROVIDER";
+  public static final String SS_PROVIDER_PROPERTY = "SS_PROVIDER";  
+
+  //generic secondary structure provider options 
+  public static final String SS_ALL_PROVIDERS = "All";  
+  public static final String SS_NONE_PROVIDER = "None";
 }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 684e355..7a5e47a 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -71,6 +71,7 @@ import jalview.structure.CommandListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
+import jalview.util.Constants;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
@@ -779,7 +780,7 @@ public abstract class AlignmentViewport
     if(aa!=null) {
       sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa);
       if(sources != null) {
-        sources.add(0,MessageManager.getString("option.ss_providers_all"));
+        sources.add(0,Constants.SS_ALL_PROVIDERS);
         viewStyle.setSecondaryStructureSources(sources);
       }
     }
diff --git a/src/jalview/workers/SecondaryStructureConsensusThread.java b/src/jalview/workers/SecondaryStructureConsensusThread.java
index bd4b78c..6629f27 100644
--- a/src/jalview/workers/SecondaryStructureConsensusThread.java
+++ b/src/jalview/workers/SecondaryStructureConsensusThread.java
@@ -35,6 +35,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
+import jalview.util.Constants;
 import jalview.util.MessageManager;
 
 public class SecondaryStructureConsensusThread extends AlignCalcWorker
@@ -200,7 +201,7 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker
     if(aa!=null) {
       sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa);
       if(sources != null) {
-        sources.add(0, MessageManager.getString("option.ss_providers_all"));
+        sources.add(0, Constants.SS_ALL_PROVIDERS);
         alignViewport.setSecondaryStructureSources(sources);
       }
     }