Resolve #523 7 Better null checks on CIF block command skips. Also clean up <bool> == false.

johnmay · johnmay · commit 7c11ff234dc4 · 2019-01-02T22:24:07.000Z
diff --git a/storage/io/src/main/java/org/openscience/cdk/io/CIFReader.java b/storage/io/src/main/java/org/openscience/cdk/io/CIFReader.java
@@ -188,16 +188,12 @@ private IChemFile readChemFile(IChemFile file) throws IOException {
                     // skip command
                     logger.warn("Skipping command: ", command);
                     line = input.readLine();
-                    if (line.startsWith(";")) {
+                    if (line != null && line.startsWith(";")) {
                         logger.debug("Skipping block content");
-                        line = input.readLine();
-                        if (line != null) line = line.trim();
-                        while (!line.equals(";")) {
-                            line = input.readLine();
-                            if (line != null) line = line.trim();
+                        while ((line = input.readLine()) != null &&
+                               !line.startsWith(";")) {
                             logger.debug("Skipping block line: ", line);
                         }
-                        line = input.readLine();
                     }
                 }
             }
@@ -336,7 +332,7 @@ private String processAtomLoopBlock(String firstLine) throws IOException {
             }
             line = input.readLine().trim();
         }
-        if (hasParsableInformation == false) {
+        if (!hasParsableInformation) {
             logger.info("No parsable info found");
             return skipLoopBody(line);
         } else {

Original file line number	Diff line number	Diff line change
`@@ -188,16 +188,12 @@ private IChemFile readChemFile(IChemFile file) throws IOException {`
`188`	`188`	`// skip command`
`189`	`189`	`logger.warn("Skipping command: ", command);`
`190`	`190`	`line = input.readLine();`
`191`		`- if (line.startsWith(";")) {`
	`191`	`+ if (line != null && line.startsWith(";")) {`
`192`	`192`	`logger.debug("Skipping block content");`
`193`		`- line = input.readLine();`
`194`		`- if (line != null) line = line.trim();`
`195`		`- while (!line.equals(";")) {`
`196`		`- line = input.readLine();`
`197`		`- if (line != null) line = line.trim();`
	`193`	`+ while ((line = input.readLine()) != null &&`
	`194`	`+ !line.startsWith(";")) {`
`198`	`195`	`logger.debug("Skipping block line: ", line);`
`199`	`196`	`}`
`200`		`- line = input.readLine();`
`201`	`197`	`}`
`202`	`198`	`}`
`203`	`199`	`}`
`@@ -336,7 +332,7 @@ private String processAtomLoopBlock(String firstLine) throws IOException {`
`336`	`332`	`}`
`337`	`333`	`line = input.readLine().trim();`
`338`	`334`	`}`
`339`		`- if (hasParsableInformation == false) {`
	`335`	`+ if (!hasParsableInformation) {`
`340`	`336`	`logger.info("No parsable info found");`
`341`	`337`	`return skipLoopBody(line);`
`342`	`338`	`} else {`