fix entity parsing

sbittrich · sbittrich · commit e9c59f677f33 · 2021-01-26T11:10:00.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/StructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/StructureConsumerImpl.java
@@ -1315,23 +1315,23 @@ private void addAncilliaryEntityData(int asymRowIndex, EntityInfo entityInfo) {
         // This is a potentially huge assumption...
 
         for (int rowIndex = 0; rowIndex < entitySrcGen.getRowCount(); rowIndex++) {
-            if (entitySrcGen.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {
+            if (!entitySrcGen.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {
                 continue;
             }
 
             addInformationFromEntitySrcGen(rowIndex, entityInfo);
         }
 
         for (int rowIndex = 0; rowIndex < entitySrcNat.getRowCount(); rowIndex++) {
-            if (entitySrcNat.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {
+            if (!entitySrcNat.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {
                 continue;
             }
 
             addInformationFromEntitySrcNat(rowIndex, entityInfo);
         }
 
         for (int rowIndex = 0; rowIndex < entitySrcSyn.getRowCount(); rowIndex++) {
-            if (entitySrcSyn.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {
+            if (!entitySrcSyn.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {
                 continue;
             }
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java
@@ -98,8 +98,6 @@ public void testEntityId() throws IOException, StructureException {
 		assertArrayEquals(descriptionInformation, testDescInfo);
 		assertArrayEquals(typeInformation, testTypeInfo);
 		// Now check these work too
-		System.out.println(Arrays.toString(geneSourceSciName));
-		System.out.println(Arrays.toString(testGeneSourceSciName));
 		assertArrayEquals(geneSourceSciName, testGeneSourceSciName);
 		assertArrayEquals(geneSourceTaxId, testGeneSourceTaxId);
 		assertArrayEquals(hostOrganismSciName, testHostOrganismSciName);

Original file line number	Diff line number	Diff line change
`@@ -1315,23 +1315,23 @@ private void addAncilliaryEntityData(int asymRowIndex, EntityInfo entityInfo) {`
`1315`	`1315`	`// This is a potentially huge assumption...`
`1316`	`1316`
`1317`	`1317`	`for (int rowIndex = 0; rowIndex < entitySrcGen.getRowCount(); rowIndex++) {`
`1318`		`- if (entitySrcGen.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {`
	`1318`	`+ if (!entitySrcGen.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {`
`1319`	`1319`	`continue;`
`1320`	`1320`	`}`
`1321`	`1321`
`1322`	`1322`	`addInformationFromEntitySrcGen(rowIndex, entityInfo);`
`1323`	`1323`	`}`
`1324`	`1324`
`1325`	`1325`	`for (int rowIndex = 0; rowIndex < entitySrcNat.getRowCount(); rowIndex++) {`
`1326`		`- if (entitySrcNat.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {`
	`1326`	`+ if (!entitySrcNat.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {`
`1327`	`1327`	`continue;`
`1328`	`1328`	`}`
`1329`	`1329`
`1330`	`1330`	`addInformationFromEntitySrcNat(rowIndex, entityInfo);`
`1331`	`1331`	`}`
`1332`	`1332`
`1333`	`1333`	`for (int rowIndex = 0; rowIndex < entitySrcSyn.getRowCount(); rowIndex++) {`
`1334`		`- if (entitySrcSyn.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {`
	`1334`	`+ if (!entitySrcSyn.getEntityId().get(rowIndex).equals(structAsym.getEntityId().get(asymRowIndex))) {`
`1335`	`1335`	`continue;`
`1336`	`1336`	`}`
`1337`	`1337`