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More manual fixes
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‎_wikis/BioJava:CookBook3:Stockholm.md‎

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Original file line numberDiff line numberDiff line change
@@ -14,97 +14,105 @@ multiple structure objects file, or an InputStream.
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### To read a single object from a file, you can simply write
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```java public static void main(String[] args){
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`   try {`
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`       StockholmFileParser parser = new StockholmFileParser();`
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`       String pathName= "stockholmFilePathAndName";`
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`       StockholmStructure structure = parser.parse(pathName);`
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`           `
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`       //use read structures`
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`           `
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`   } catch (IOException e) {`
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`       e.printStackTrace();`
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`   } catch (Exception e) {`
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`       e.printStackTrace();`
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`   }`
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} ```
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```java
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public static void main(String[] args){
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   try {
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       StockholmFileParser parser = new StockholmFileParser();
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       String pathName= "stockholmFilePathAndName";
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       StockholmStructure structure = parser.parse(pathName);
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       //use read structures
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   } catch (IOException e) {
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       e.printStackTrace();
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   } catch (Exception e) {
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       e.printStackTrace();
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   }
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}
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```
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### Also you can read multiple alignments within the same file as follows
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```java public static void main(String[] args){
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`   try {`
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`       StockholmFileParser parser = new StockholmFileParser();`
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`       String sourcePath=settingsManager.getSourcePath();`
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`       String fileName= settingsManager.getFileName();`
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`       FileInputStream inStream = new FileInputStream(new File(sourcePath,fileName));`
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`       String outputPath=settingsManager.getOutputPath();`
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`       parser.parse(inStream,STRUCTURES_TO_SKIP);//if you don't want to start from first structure`
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`       do {`
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`           structures = parser.parse(inStream, MAX_PER_ITERATION);`
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`           for (int i = 0; i < structures.size(); i++) {`
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`               StockholmStructure structure = structures.get(i);`
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`               List`<AbstractSequence<? extends AbstractCompound>`> sequences = structure.getBioSequences(true);`
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`               final String accessionNumber = structure.getFileAnnotation().getAccessionNumber();`
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`               final String identification = structure.getFileAnnotation().getIdentification().toString();`
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`               manageRelatedSequences(accessionNumber, identification,sequences);`
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`           }`
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`       } while (structures.size()== MAX_PER_ITERATION);`
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`   } catch (FileNotFoundException e) {`
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`       e.printStackTrace();`
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`   } catch (IOException e) {`
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`       e.printStackTrace();`
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`   } catch (Exception e) {`
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`       e.printStackTrace();`
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`   }`
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} ```
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```java
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public static void main(String[] args){
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   try {
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       StockholmFileParser parser = new StockholmFileParser();
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       String sourcePath=settingsManager.getSourcePath();
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       String fileName= settingsManager.getFileName();
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       FileInputStream inStream = new FileInputStream(new File(sourcePath,fileName));
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       String outputPath=settingsManager.getOutputPath();
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       parser.parse(inStream,STRUCTURES_TO_SKIP);//if you don't want to start from first structure
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       do {
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           structures = parser.parse(inStream, MAX_PER_ITERATION);
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           for (int i = 0; i < structures.size(); i++) {
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               StockholmStructure structure = structures.get(i);
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               List<AbstractSequence<? extends AbstractCompound>> sequences = structure.getBioSequences(true);
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               final String accessionNumber = structure.getFileAnnotation().getAccessionNumber();
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               final String identification = structure.getFileAnnotation().getIdentification().toString();
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               manageRelatedSequences(accessionNumber, identification,sequences);
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           }
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       } while (structures.size()== MAX_PER_ITERATION);
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   } catch (FileNotFoundException e) {
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       e.printStackTrace();
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   } catch (IOException e) {
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       e.printStackTrace();
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   } catch (Exception e) {
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       e.printStackTrace();
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   }
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}
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```
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### Some times you don't have a reference to the file or input stream
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Some times you use the parser in a place other than where it was
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created.
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For example, you can create a StockholmFileParser in a function ```java
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For example, you can create a StockholmFileParser in a function
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```java
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`   public StockholmFileParser getStockholmFileParser(String filePathName) {`
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`       StockholmFileParser parser = new StockholmFileParser();`
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`       try {`
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`           parser.parse(filePathName, 0);`
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`       } catch (ParserException e) {`
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`           e.printStackTrace();`
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`       } catch (IOException e) {`
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`           e.printStackTrace();`
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`       }`
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`       return parser;`
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`   }`
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   public StockholmFileParser getStockholmFileParser(String filePathName) {
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       StockholmFileParser parser = new StockholmFileParser();
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       try {
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           parser.parse(filePathName, 0);
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       } catch (ParserException e) {
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           e.printStackTrace();
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       } catch (IOException e) {
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           e.printStackTrace();
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       }
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       return parser;
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   }
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```
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Then you use the created parser in another function, where you don't
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have a reference to its underling data source ```java
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`   public void useParser(StockholmFileParser parser) {`
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`       final int MAX_PER_ITTERATION = 10;`
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`       List`<StockholmStructure>` structures;`
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`       long count= 0;`
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`       int successfullyRead = 0;`
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`       do {`
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`           try {`
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`               structures = parser.parseNext(MAX_PER_ITTERATION);`
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`               successfullyRead = structures.size();`
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`           } catch (IOException e) {`
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`               e.printStackTrace();`
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`           }`
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`           count += successfullyRead;`
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`           System.out.println("reached "+count);`
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`           `
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`           //use read structures`
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`           `
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`       } while (successfullyRead== MAX_PER_ITTERATION);`
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`       System.out.println("TOTAL COUNT = "+count);`
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`   }`
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have a reference to its underling data source
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```java
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   public void useParser(StockholmFileParser parser) {
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       final int MAX_PER_ITTERATION = 10;
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       List<StockholmStructure> structures;
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       long count= 0;
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       int successfullyRead = 0;
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       do {
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           try {
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               structures = parser.parseNext(MAX_PER_ITTERATION);
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               successfullyRead = structures.size();
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           } catch (IOException e) {
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               e.printStackTrace();
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           }
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           count += successfullyRead;
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           System.out.println("reached "+count);
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           //use read structures
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       } while (successfullyRead== MAX_PER_ITTERATION);
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       System.out.println("TOTAL COUNT = "+count);
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   }
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```

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