X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=56e9fa10ada182f95b7bcbb45b4a0c8c39dbde43;hb=1ef93cb2817f75699773f049b8d25e5b509c2830;hp=4916bb3b44b7bedda13e5869b2cdda36920e5c47;hpb=0424fec4a6d71684f56978f61eadd4ceb0652a60;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 4916bb3..56e9fa1 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,6 +20,12 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+import java.util.Locale;
+
 import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
@@ -32,11 +38,6 @@ import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 import jalview.util.Platform;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
@@ -152,17 +153,21 @@ public class AppletFormatAdapter
   {
     return readFile(null, file, sourceType, fileFormat);
   }
-  
-  public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
-          FileFormatI fileFormat) throws IOException
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat)
+          throws IOException
+  {
+    return readFile(selectedFile, file, sourceType, fileFormat, null);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          StructureImportSettings.TFType tempfacType) throws IOException
   {
 
     this.selectedFile = selectedFile;
-    if (selectedFile != null)
-    {
-      this.inFile = selectedFile.getPath();
-    }
-    this.inFile = file;
+    this.inFile = selectedFile != null ? selectedFile.getPath() : file;
     try
     {
       if (fileFormat.isStructureFile())
@@ -174,10 +179,16 @@ public class AppletFormatAdapter
                         .toString());
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
+        if (tempfacType != null)
+        {
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+        }
         if (isParseWithJMOL)
         {
           // needs a File option
-          alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
+          alignFile = new JmolParser(
+                  selectedFile == null ? inFile : selectedFile, sourceType,
+                  StructureImportSettings.getTemperatureFactorType());
         }
         else
         {
@@ -190,9 +201,12 @@ public class AppletFormatAdapter
         ((StructureFile) alignFile).setDbRefType(
                 FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
       }
-      else if (selectedFile != null) {
-        alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
-      } else 
+      else if (selectedFile != null)
+      {
+        alignFile = fileFormat
+                .getReader(new FileParse(selectedFile, sourceType));
+      }
+      else
       {
         // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
         alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
@@ -201,7 +215,7 @@ public class AppletFormatAdapter
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + fileFormat
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '" + fileFormat
               + "' reader.\n" + e);
 
       if (e.getMessage() != null
@@ -283,7 +297,7 @@ public class AppletFormatAdapter
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '" + format
               + "' reader.\n" + e);
 
       if (e.getMessage() != null
@@ -410,13 +424,13 @@ public class AppletFormatAdapter
       String afileresp = afile.print(seqs, jvsuffix);
       if (afile.hasWarningMessage())
       {
-        System.err.println("Warning raised when writing as " + format
+        jalview.bin.Console.errPrintln("Warning raised when writing as " + format
                 + " : " + afile.getWarningMessage());
       }
       return afileresp;
     } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '"
+      jalview.bin.Console.errPrintln("Failed to write alignment as a '"
               + format.getName() + "' file\n");
       e.printStackTrace();
     }
@@ -424,26 +438,26 @@ public class AppletFormatAdapter
     return null;
   }
 
-
   /**
    * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
    * data
    * 
    * BH 2018 allows File or String, and can return RELATIVE_URL
    *
-   * @param dataObject File or String
+   * @param dataObject
+   *          File or String
    * @return the protocol for the input data
    */
   public static DataSourceType checkProtocol(Object dataObject)
   {
-    if(dataObject instanceof File)
+    if (dataObject instanceof File)
     {
       return DataSourceType.FILE;
     }
-    
+
     String data = dataObject.toString();
     DataSourceType protocol = DataSourceType.PASTE;
-    String ft = data.toLowerCase().trim();
+    String ft = data.toLowerCase(Locale.ROOT).trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
@@ -474,7 +488,7 @@ public class AppletFormatAdapter
       {
         try
         {
-          System.out.println("Reading file: " + f);
+          jalview.bin.Console.outPrintln("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
           Runtime r = Runtime.getRuntime();
           System.gc();
@@ -488,36 +502,36 @@ public class AppletFormatAdapter
           memf += r.totalMemory() - r.freeMemory();
           if (al != null)
           {
-            System.out.println("Alignment contains " + al.getHeight()
+            jalview.bin.Console.outPrintln("Alignment contains " + al.getHeight()
                     + " sequences and " + al.getWidth() + " columns.");
             try
             {
-              System.out.println(new AppletFormatAdapter()
+              jalview.bin.Console.outPrintln(new AppletFormatAdapter()
                       .formatSequences(FileFormat.Fasta, al, true));
             } catch (Exception e)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
           else
           {
-            System.out.println("Couldn't read alignment");
+            jalview.bin.Console.outPrintln("Couldn't read alignment");
           }
-          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
-          System.out.println(
+          jalview.bin.Console.outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
+          jalview.bin.Console.outPrintln(
                   "Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
-          System.err.println("Exception when dealing with " + i
+          jalview.bin.Console.errPrintln("Exception when dealing with " + i
                   + "'th argument: " + args[i] + "\n" + e);
         }
       }
       else
       {
-        System.err.println("Ignoring argument '" + args[i] + "' (" + i
+        jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] + "' (" + i
                 + "'th)- not a readable file.");
       }
       i++;
@@ -545,7 +559,7 @@ public class AppletFormatAdapter
     DataSourceType protocol = null;
     if (debug)
     {
-      System.out.println("resolving datasource started with:\n>>file\n"
+      jalview.bin.Console.outPrintln("resolving datasource started with:\n>>file\n"
               + file + ">>endfile");
     }
 
@@ -563,7 +577,7 @@ public class AppletFormatAdapter
       }
       if (debug)
       {
-        System.err.println("Resource '" + file + "' was "
+        jalview.bin.Console.errPrintln("Resource '" + file + "' was "
                 + (rtn ? "" : "not") + " located by classloader.");
       }
       if (rtn)
@@ -591,7 +605,7 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "Trying to get contents of resource as " + protocol + ":");
       }
       fp = new FileParse(file, protocol);
@@ -603,14 +617,14 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.out.println("Successful.");
+          jalview.bin.Console.outPrintln("Successful.");
         }
       }
     } catch (Exception e)
     {
       if (debug)
       {
-        System.err.println("Exception when accessing content: " + e);
+        jalview.bin.Console.errPrintln("Exception when accessing content: " + e);
       }
       fp = null;
     }
@@ -618,7 +632,7 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println("Accessing as paste.");
+        jalview.bin.Console.outPrintln("Accessing as paste.");
       }
       protocol = DataSourceType.PASTE;
       fp = null;
@@ -631,7 +645,7 @@ public class AppletFormatAdapter
         }
       } catch (Exception e)
       {
-        System.err.println("Failed to access content as paste!");
+        jalview.bin.Console.errPrintln("Failed to access content as paste!");
         e.printStackTrace();
         fp = null;
       }
@@ -653,20 +667,20 @@ public class AppletFormatAdapter
         {
           if (debug)
           {
-            System.out.println("Format not identified. Inaccessible file.");
+            jalview.bin.Console.outPrintln("Format not identified. Inaccessible file.");
           }
           return null;
         }
         if (debug)
         {
-          System.out.println("Format identified as " + idformat
+          jalview.bin.Console.outPrintln("Format identified as " + idformat
                   + "and expected as " + format);
         }
         if (idformat.equals(format))
         {
           if (debug)
           {
-            System.out.println("Protocol identified as " + protocol);
+            jalview.bin.Console.outPrintln("Protocol identified as " + protocol);
           }
           return protocol;
         }
@@ -684,7 +698,7 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.err.println("File deemed not accessible via " + protocol);
+          jalview.bin.Console.errPrintln("File deemed not accessible via " + protocol);
           e.printStackTrace();
         }
       }