JAL-2089 Merge branch releases/Release_2_10_Branch to master

[jalview.git] / src / jalview / structure / StructureImportSettings.java

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
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+++ b/src/jalview/structure/StructureImportSettings.java
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+/*
+ * 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.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
+{
+  /**
+   * 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;
+
+  /**
+   * Set true to predict secondary structure (using JMol for protein, Annotate3D
+   * for RNA)
+   */
+  private static 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 static boolean showSeqFeatures = true;
+
+  public enum StructureParser
+  {
+    JMOL_PARSER, JALVIEW_PARSER
+  }
+
+  /**
+   * Determines the default file format for structure files to be downloaded
+   * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
+   */
+  private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;
+
+  /**
+   * Determines the parser used for parsing PDB format file. Possible options
+   * are : JMolParser|JalveiwParser
+   */
+  private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
+
+  public static void addSettings(boolean addAlignmentAnnotations,
+          boolean processSecStr, boolean externalSecStr)
+  {
+    StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
+    StructureImportSettings.processSecStr = processSecStr;
+    StructureImportSettings.externalSecondaryStructure = externalSecStr;
+    StructureImportSettings.showSeqFeatures = true;
+  }
+
+  public static boolean isVisibleChainAnnotation()
+  {
+    return visibleChainAnnotation;
+  }
+
+  public static void setVisibleChainAnnotation(
+          boolean visibleChainAnnotation)
+  {
+    StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
+  }
+
+  public static boolean isProcessSecondaryStructure()
+  {
+    return processSecStr;
+  }
+
+  public static void setProcessSecondaryStructure(
+          boolean processSecondaryStructure)
+  {
+    StructureImportSettings.processSecStr = processSecondaryStructure;
+  }
+
+  public static boolean isExternalSecondaryStructure()
+  {
+    return externalSecondaryStructure;
+  }
+
+  public static void setExternalSecondaryStructure(
+          boolean externalSecondaryStructure)
+  {
+    StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
+  }
+
+  public static boolean isShowSeqFeatures()
+  {
+    return showSeqFeatures;
+  }
+
+  public static void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    StructureImportSettings.showSeqFeatures = showSeqFeatures;
+  }
+
+  public static String getDefaultStructureFileFormat()
+  {
+    return defaultStructureFileFormat.toString();
+  }
+
+  public static void setDefaultStructureFileFormat(
+          String defaultStructureFileFormat)
+  {
+    StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+            .valueOf(defaultStructureFileFormat.toUpperCase());
+  }
+
+  public static String getDefaultPDBFileParser()
+  {
+    return defaultPDBFileParser.toString();
+  }
+
+  public static void setDefaultPDBFileParser(
+          StructureParser defaultPDBFileParser)
+  {
+    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
+  }
+
+  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+  {
+    StructureImportSettings.defaultPDBFileParser = StructureParser
+            .valueOf(defaultPDBFileParser.toUpperCase());
+  }
+
+}