JAL-2349 JAL-3855 formatting

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 7a052da..10f87b1 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -3,6 +3,9 @@
  */
 package jalview.renderer;
 
+import java.awt.Color;
+import java.awt.Graphics;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -12,9 +15,6 @@ import jalview.datamodel.ContactRange;
 import jalview.datamodel.HiddenColumns;
 import jalview.renderer.api.AnnotationRowRendererI;
 
-import java.awt.Color;
-import java.awt.Graphics;
-
 /**
  * @author jprocter
  *
@@ -24,10 +24,10 @@ public class ContactMapRenderer implements AnnotationRowRendererI
 
   @Override
   public void renderRow(Graphics g, int charWidth, int charHeight,
-          boolean hasHiddenColumns, AlignViewportI viewport, HiddenColumns hiddenColumns,
-          ColumnSelection columnSelection, AlignmentAnnotation _aa,
-          Annotation[] aa_annotations, int sRes, int eRes, float min,
-          float max, int y)
+          boolean hasHiddenColumns, AlignViewportI viewport,
+          HiddenColumns hiddenColumns, ColumnSelection columnSelection,
+          AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
+          int eRes, float min, float max, int y)
   {
     if (sRes > aa_annotations.length)
     {

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index 97eacab..e0ab54d 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -21,45 +21,33 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import com.stevesoft.pat.Regex;
+
 import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ContactMatrix;
 import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.PDBFeatureSettings;
-import jalview.javascript.json.JSON;
-import jalview.structure.StructureImportSettings;
-import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
-import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.jmol.adapter.readers.simple.JSONReader;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * @author JimP
  * 
@@ -188,7 +176,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     try
     {
       File tmpFile = File.createTempFile(id, ".cif");
-      Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
+      Console.debug("Retrieving structure file for " + id + " from "
+              + alphaFoldCif);
       UrlDownloadClient.download(alphaFoldCif, tmpFile);
 
       // may not need this check ?
@@ -216,20 +205,23 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       if (retrievalUrl != null)
       {
         // manufacture the PAE url from a url like ...-model-vN.cif
-        paeURL = retrievalUrl.replace("model","predicted_aligned_error").replace(".cif",".json");
+        paeURL = retrievalUrl.replace("model", "predicted_aligned_error")
+                .replace(".cif", ".json");
       }
-      Console.debug("Downloading pae from " + paeURL
-              + " to " + pae.toString() + "");
+      Console.debug("Downloading pae from " + paeURL + " to "
+              + pae.toString() + "");
 
-      try {
-        UrlDownloadClient.download(paeURL, pae);        
-      if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
+      try
       {
-        Console.warn("Couln't import contact matrix from " + paeURL
-                + " (stored in " + pae.toString() + ")");
-      }
-      } catch (Exception pae_ex) {
-        Console.debug("Couldn't download PAE",pae_ex);
+        UrlDownloadClient.download(paeURL, pae);
+        if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
+        {
+          Console.warn("Couln't import contact matrix from " + paeURL
+                  + " (stored in " + pae.toString() + ")");
+        }
+      } catch (Exception pae_ex)
+      {
+        Console.debug("Couldn't download PAE", pae_ex);
       }
 
     } catch (Exception ex) // Problem parsing PDB file
@@ -245,16 +237,17 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   {
     FileInputStream pae_input = new FileInputStream(pae);
 
-    List<Object> pae_obj = (List<Object>) Platform
-            .parseJSON(pae_input);
+    List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
     if (pae_obj == null)
     {
       return false;
     }
     ContactMatrixI matrix = new PAEContactMatrix(
-            pdbAlignment.getSequenceAt(0), (Map<String, Object>)pae_obj.get(0));
+            pdbAlignment.getSequenceAt(0),
+            (Map<String, Object>) pae_obj.get(0));
 
-    pdbAlignment.getSequenceAt(0).addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+    pdbAlignment.getSequenceAt(0)
+            .addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
     return true;
   }
 

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index d00abb1..4b1f7e9 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -27,16 +27,6 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
-import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatI;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MapList;
-
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Iterator;
@@ -47,6 +37,16 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
 /**
  * Unit tests for Alignment datamodel.
  *