X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureImportSettings.java;h=b5672ab6c2fb5454facbfdb72e90db7928be63e6;hb=e99c06994dd1e8e0d1740b7eaa89cd2c63861e89;hp=b23fd53cf9d16a259731ae6e5fea6f3bd65a35f7;hpb=0bec4854366c4bc4608ed0d7dc1506fc6afe2285;p=jalview.git

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index b23fd53..b5672ab 100644
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -1,103 +1,168 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.structure;
 
-import jalview.datamodel.DBRefSource;
-
-public class StructureImportSettings
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+
+/**
+ * bean holding settings for structure IO. TODO: tests for validation of values
+ * TODO: tests for race conditions (all fields are static, is that correct ?)
+ * 
+ * @author tcofoegbu
+ *
+ */
+public class StructureImportSettings implements ApplicationSingletonI
 {
+
+  private StructureImportSettings()
+  {
+    // private singleton
+  }
+
+  private static StructureImportSettings getInstance()
+  {
+    return (StructureImportSettings) ApplicationSingletonProvider
+            .getInstance(StructureImportSettings.class);
+  }
+
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
    */
-  private static boolean visibleChainAnnotation = false;
+  private boolean visibleChainAnnotation = false;
 
   /**
    * Set true to predict secondary structure (using JMol for protein, Annotate3D
    * for RNA)
    */
-  private static boolean predictSecStr = false;
+  private boolean processSecStr = false;
 
   /**
    * Set true (with predictSecondaryStructure=true) to predict secondary
    * structure using an external service (currently Annotate3D for RNA only)
    */
-  private static boolean externalSecondaryStructure = false;
+  private boolean externalSecondaryStructure = false;
+
+  private boolean showSeqFeatures = true;
 
-  private static boolean showSeqFeatures = true;
+  public enum StructureParser
+  {
+    JMOL_PARSER, JALVIEW_PARSER
+  }
 
-  private static boolean processHETATMs = false;
+  /**
+   * Determines the default file format for structure files to be downloaded
+   * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
+   */
+  private PDBEntry.Type defaultStructureFileFormat = Type.PDB;
 
-  private static String currentDefaultFormat = DBRefSource.PDB;
+  /**
+   * Determines the parser used for parsing PDB format file. Possible options
+   * are : JMolParser|JalveiwParser
+   */
+  private StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
 
   public static void addSettings(boolean addAlignmentAnnotations,
-          boolean predictSecStr, boolean externalSecStr)
+          boolean processSecStr, boolean externalSecStr)
   {
-    StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
-    StructureImportSettings.predictSecStr = predictSecStr;
-    StructureImportSettings.externalSecondaryStructure = externalSecStr;
-    StructureImportSettings.showSeqFeatures = true;
+    StructureImportSettings s = getInstance();
+    s.visibleChainAnnotation = addAlignmentAnnotations;
+    s.processSecStr = processSecStr;
+    s.externalSecondaryStructure = externalSecStr;
+    s.showSeqFeatures = true;
   }
 
   public static boolean isVisibleChainAnnotation()
   {
-    return visibleChainAnnotation;
+    return getInstance().visibleChainAnnotation;
   }
 
   public static void setVisibleChainAnnotation(
           boolean visibleChainAnnotation)
   {
-    StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
+    getInstance().visibleChainAnnotation = visibleChainAnnotation;
   }
 
-  public static boolean isPredictSecondaryStructure()
+  public static boolean isProcessSecondaryStructure()
   {
-    return predictSecStr;
+    return getInstance().processSecStr;
   }
 
-  public static void setPredictSecondaryStructure(
-          boolean predictSecondaryStructure)
+  public static void setProcessSecondaryStructure(
+          boolean processSecondaryStructure)
   {
-    StructureImportSettings.predictSecStr = predictSecondaryStructure;
+    getInstance().processSecStr = processSecondaryStructure;
   }
 
   public static boolean isExternalSecondaryStructure()
   {
-    return externalSecondaryStructure;
+    return getInstance().externalSecondaryStructure;
   }
 
   public static void setExternalSecondaryStructure(
           boolean externalSecondaryStructure)
   {
-    StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
+    getInstance().externalSecondaryStructure = externalSecondaryStructure;
   }
 
   public static boolean isShowSeqFeatures()
   {
-    return showSeqFeatures;
+    return getInstance().showSeqFeatures;
   }
 
   public static void setShowSeqFeatures(boolean showSeqFeatures)
   {
-    StructureImportSettings.showSeqFeatures = showSeqFeatures;
+    getInstance().showSeqFeatures = showSeqFeatures;
+  }
+
+  public static PDBEntry.Type getDefaultStructureFileFormat()
+  {
+    return getInstance().defaultStructureFileFormat;
   }
 
-  public static String getCurrentDefaultFormat()
+  public static void setDefaultStructureFileFormat(
+          String defaultStructureFileFormat)
   {
-    return currentDefaultFormat;
+    getInstance().defaultStructureFileFormat = PDBEntry.Type
+            .valueOf(defaultStructureFileFormat.toUpperCase());
   }
 
-  public static void setCurrentDefaultFormat(String currentDefaultFormat)
+  public static String getDefaultPDBFileParser()
   {
-    StructureImportSettings.currentDefaultFormat = currentDefaultFormat;
+    return getInstance().defaultPDBFileParser.toString();
   }
 
-  public static boolean isProcessHETATMs()
+  public static void setDefaultPDBFileParser(
+          StructureParser defaultPDBFileParser)
   {
-    return processHETATMs;
+    getInstance().defaultPDBFileParser = defaultPDBFileParser;
   }
 
-  public static void setProcessHETATMs(boolean processHETATMs)
+  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
   {
-    StructureImportSettings.processHETATMs = processHETATMs;
+    getInstance().defaultPDBFileParser = StructureParser
+            .valueOf(defaultPDBFileParser.toUpperCase());
   }
 
 }