Merge pull request biojava#96 from pwrose/master

pwrose · pwrose · commit d79be3f1b6c5 · 2014-03-05T16:54:43.000-08:00
Added Java Bean for mmcif category _struct_conn
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileConvert.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/io/FileConvert.java
@@ -54,13 +54,13 @@ public class FileConvert {
 	// Locale should be english, e.g. in DE separator is "," -> PDB files have "." !
 	static DecimalFormat d3 = (DecimalFormat)NumberFormat.getInstance(java.util.Locale.UK);
 	static {
-		d3.setMaximumIntegerDigits(3);
+		d3.setMaximumIntegerDigits(4);
 		d3.setMinimumFractionDigits(3);
 		d3.setMaximumFractionDigits(3);
 	}
 	static DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(java.util.Locale.UK);
 	static {
-		d2.setMaximumIntegerDigits(2);
+		d2.setMaximumIntegerDigits(3);
 		d2.setMinimumFractionDigits(2);
 		d2.setMaximumFractionDigits(2);
 	}
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/io/MMCIFFileReader.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/io/MMCIFFileReader.java
@@ -147,7 +147,7 @@ public Structure getStructure(File filename) throws IOException {
 
 
 
-	private Structure parseFromInputStream(InputStream inStream) throws IOException{
+	public Structure parseFromInputStream(InputStream inStream) throws IOException{
 
 		MMcifParser parser = new SimpleMMcifParser();
 
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -52,13 +52,11 @@
 import org.biojava.bio.structure.StructureTools;
 import org.biojava.bio.structure.UnknownPdbAminoAcidException;
 import org.biojava.bio.structure.io.FileParsingParameters;
-
 import org.biojava.bio.structure.io.PDBParseException;
 import org.biojava.bio.structure.io.SeqRes2AtomAligner;
 import org.biojava.bio.structure.io.mmcif.model.AtomSite;
 import org.biojava.bio.structure.io.mmcif.model.AuditAuthor;
 import org.biojava.bio.structure.io.mmcif.model.ChemComp;
-
 import org.biojava.bio.structure.io.mmcif.model.ChemCompAtom;
 import org.biojava.bio.structure.io.mmcif.model.ChemCompBond;
 import org.biojava.bio.structure.io.mmcif.model.ChemCompDescriptor;
@@ -81,6 +79,7 @@
 import org.biojava.bio.structure.io.mmcif.model.Refine;
 import org.biojava.bio.structure.io.mmcif.model.Struct;
 import org.biojava.bio.structure.io.mmcif.model.StructAsym;
+import org.biojava.bio.structure.io.mmcif.model.StructConn;
 import org.biojava.bio.structure.io.mmcif.model.StructKeywords;
 import org.biojava.bio.structure.io.mmcif.model.StructRef;
 import org.biojava.bio.structure.io.mmcif.model.StructRefSeq;
@@ -115,6 +114,7 @@ public class SimpleMMcifConsumer implements MMcifConsumer {
 	List<EntitySrcGen> entitySrcGens;
 	List<EntitySrcNat> entitySrcNats;
 	List<EntitySrcSyn> entitySrcSyns;
+	List<StructConn> structConn;
 
 	Map<String,String> asymStrandId;
 
@@ -677,6 +677,7 @@ public void documentStart() {
 		entitySrcGens = new ArrayList<EntitySrcGen>();
 		entitySrcNats = new ArrayList<EntitySrcNat>();
 		entitySrcSyns = new ArrayList<EntitySrcSyn>();
+		structConn = new ArrayList<StructConn>();
 	}
 
 
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/StructConn.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/model/StructConn.java

Original file line number	Diff line number	Diff line change
`@@ -147,7 +147,7 @@ public Structure getStructure(File filename) throws IOException {`
`147`	`147`
`148`	`148`
`149`	`149`
`150`		`- private Structure parseFromInputStream(InputStream inStream) throws IOException{`
	`150`	`+ public Structure parseFromInputStream(InputStream inStream) throws IOException{`
`151`	`151`
`152`	`152`	`MMcifParser parser = new SimpleMMcifParser();`
`153`	`153`