Package com.actelion.research.chem.io
Class CompoundFileHelper
- java.lang.Object
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- com.actelion.research.chem.io.CompoundFileHelper
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- Direct Known Subclasses:
FileHelper
public abstract class CompoundFileHelper extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static int
cFileTypeDataWarrior
static int
cFileTypeDataWarriorCompatibleData
static int
cFileTypeDataWarriorMacro
static int
cFileTypeDataWarriorQuery
static int
cFileTypeDataWarriorTemplate
static int
cFileTypeDataWarriorTemplateContaining
static int
cFileTypeDirectory
static int
cFileTypeGIF
static int
cFileTypeJPG
static int
cFileTypeMask
static int
cFileTypeMMTF
static int
cFileTypeMOL
static int
cFileTypeMOL2
static int
cFileTypePDB
static int
cFileTypePictureFile
static int
cFileTypePNG
static int
cFileTypeProtein
static int
cFileTypeRD
static int
cFileTypeRDV2
static int
cFileTypeRDV3
static int
cFileTypeRXN
static int
cFileTypeSD
static int
cFileTypeSDGZ
static int
cFileTypeSDV2
static int
cFileTypeSDV3
static int
cFileTypeSOM
static int
cFileTypeSVG
static int
cFileTypeText
static int
cFileTypeTextCommaSeparated
static int
cFileTypeTextTabDelimited
static int
cFileTypeUnknown
static java.lang.String
cGZipExtention
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Constructor Summary
Constructors Constructor Description CompoundFileHelper()
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description static CompoundFileFilter
createFileFilter(int filetypes, boolean isSaving)
static java.io.File
getCurrentDirectory()
int
getErrorCount()
static java.lang.String
getExtension(int filetype)
static java.lang.String
getExtension(java.io.File file)
Return the extension portion of the file's name.java.util.ArrayList<java.lang.String>
getExtensionList(int fileTypes)
static int
getFileType(java.lang.String filename)
int
getRecordCount()
java.util.ArrayList<java.lang.String>
readIDCodesFromFile()
java.util.ArrayList<java.lang.String>
readIDCodesFromFile(java.io.File file)
Reads all compounds as idcode list from the given file.java.util.ArrayList<java.lang.String[]>
readIDCodesWithNamesFromFile(java.io.File file, boolean readIDCoords)
Reads all compounds as idcode list with identifiers from the given file.java.util.ArrayList<StereoMolecule>
readStructuresFromFile(boolean readIdentifier)
java.util.ArrayList<StereoMolecule>
readStructuresFromFile(java.io.File file, boolean readIdentifier)
static java.lang.String
removeExtension(java.lang.String filePath)
Provided that filePath has a recognized extension, then the extension is removed.static java.lang.String
removePathAndExtension(java.lang.String filePath)
Provided that fileName has a leading file path, then path and separator are removed.void
saveRXNFile(Reaction rxn)
abstract java.io.File
selectFileToOpen(java.lang.String title, int filetypes)
abstract java.lang.String
selectFileToSave(java.lang.String title, int filetype, java.lang.String newFileName)
abstract java.lang.String
selectOption(java.lang.String message, java.lang.String title, java.lang.String[] option)
static void
setCurrentDirectory(java.io.File d)
abstract void
showMessage(java.lang.String message)
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Field Detail
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cFileTypeMask
public static final int cFileTypeMask
- See Also:
- Constant Field Values
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cFileTypeDataWarrior
public static final int cFileTypeDataWarrior
- See Also:
- Constant Field Values
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cFileTypeDataWarriorTemplate
public static final int cFileTypeDataWarriorTemplate
- See Also:
- Constant Field Values
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cFileTypeDataWarriorQuery
public static final int cFileTypeDataWarriorQuery
- See Also:
- Constant Field Values
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cFileTypeDataWarriorMacro
public static final int cFileTypeDataWarriorMacro
- See Also:
- Constant Field Values
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cFileTypeTextTabDelimited
public static final int cFileTypeTextTabDelimited
- See Also:
- Constant Field Values
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cFileTypeTextCommaSeparated
public static final int cFileTypeTextCommaSeparated
- See Also:
- Constant Field Values
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cFileTypeText
public static final int cFileTypeText
- See Also:
- Constant Field Values
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cFileTypeSDV3
public static final int cFileTypeSDV3
- See Also:
- Constant Field Values
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cFileTypeSDV2
public static final int cFileTypeSDV2
- See Also:
- Constant Field Values
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cFileTypeSD
public static final int cFileTypeSD
- See Also:
- Constant Field Values
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cFileTypeRXN
public static final int cFileTypeRXN
- See Also:
- Constant Field Values
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cFileTypeSOM
public static final int cFileTypeSOM
- See Also:
- Constant Field Values
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cFileTypeJPG
public static final int cFileTypeJPG
- See Also:
- Constant Field Values
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cFileTypeGIF
public static final int cFileTypeGIF
- See Also:
- Constant Field Values
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cFileTypePNG
public static final int cFileTypePNG
- See Also:
- Constant Field Values
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cFileTypeSVG
public static final int cFileTypeSVG
- See Also:
- Constant Field Values
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cFileTypePictureFile
public static final int cFileTypePictureFile
- See Also:
- Constant Field Values
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cFileTypeRDV3
public static final int cFileTypeRDV3
- See Also:
- Constant Field Values
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cFileTypeRDV2
public static final int cFileTypeRDV2
- See Also:
- Constant Field Values
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cFileTypeRD
public static final int cFileTypeRD
- See Also:
- Constant Field Values
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cFileTypeMOL
public static final int cFileTypeMOL
- See Also:
- Constant Field Values
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cFileTypeMOL2
public static final int cFileTypeMOL2
- See Also:
- Constant Field Values
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cFileTypePDB
public static final int cFileTypePDB
- See Also:
- Constant Field Values
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cFileTypeMMTF
public static final int cFileTypeMMTF
- See Also:
- Constant Field Values
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cFileTypeProtein
public static final int cFileTypeProtein
- See Also:
- Constant Field Values
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cFileTypeSDGZ
public static final int cFileTypeSDGZ
- See Also:
- Constant Field Values
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cFileTypeUnknown
public static final int cFileTypeUnknown
- See Also:
- Constant Field Values
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cFileTypeDirectory
public static final int cFileTypeDirectory
- See Also:
- Constant Field Values
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cGZipExtention
public static final java.lang.String cGZipExtention
- See Also:
- Constant Field Values
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cFileTypeDataWarriorCompatibleData
public static final int cFileTypeDataWarriorCompatibleData
- See Also:
- Constant Field Values
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cFileTypeDataWarriorTemplateContaining
public static final int cFileTypeDataWarriorTemplateContaining
- See Also:
- Constant Field Values
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Method Detail
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selectOption
public abstract java.lang.String selectOption(java.lang.String message, java.lang.String title, java.lang.String[] option)
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selectFileToOpen
public abstract java.io.File selectFileToOpen(java.lang.String title, int filetypes)
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selectFileToSave
public abstract java.lang.String selectFileToSave(java.lang.String title, int filetype, java.lang.String newFileName)
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showMessage
public abstract void showMessage(java.lang.String message)
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getCurrentDirectory
public static java.io.File getCurrentDirectory()
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setCurrentDirectory
public static void setCurrentDirectory(java.io.File d)
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readStructuresFromFile
public java.util.ArrayList<StereoMolecule> readStructuresFromFile(boolean readIdentifier)
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readIDCodesFromFile
public java.util.ArrayList<java.lang.String> readIDCodesFromFile()
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readStructuresFromFile
public java.util.ArrayList<StereoMolecule> readStructuresFromFile(java.io.File file, boolean readIdentifier)
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readIDCodesFromFile
public java.util.ArrayList<java.lang.String> readIDCodesFromFile(java.io.File file)
Reads all compounds as idcode list from the given file.- Parameters:
file
- SD- or DataWarrior file- Returns:
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readIDCodesWithNamesFromFile
public java.util.ArrayList<java.lang.String[]> readIDCodesWithNamesFromFile(java.io.File file, boolean readIDCoords)
Reads all compounds as idcode list with identifiers from the given file. Therefore, it asks for an identifier column.- Parameters:
file
- if null the user is asked for a filereadIDCoords
- if true, then the id-coords are SPACE delimited attached to the idcode- Returns:
- list of String[2] with idcode (index 0) and molecule name (index 1)
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getRecordCount
public int getRecordCount()
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getErrorCount
public int getErrorCount()
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createFileFilter
public static CompoundFileFilter createFileFilter(int filetypes, boolean isSaving)
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getExtension
public static java.lang.String getExtension(java.io.File file)
Return the extension portion of the file's name. Known joint extensions (currently only ".sdf.gz") are returned where they exist.- Returns:
- extension without the dot
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removePathAndExtension
public static java.lang.String removePathAndExtension(java.lang.String filePath)
Provided that fileName has a leading file path, then path and separator are removed. Provided that fileName has a recognized extension, then the extension is removed.- Parameters:
filePath
- file name with or without complete path and with or without extension- Returns:
- naked file name without leading path and extension
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removeExtension
public static java.lang.String removeExtension(java.lang.String filePath)
Provided that filePath has a recognized extension, then the extension is removed.- Parameters:
filePath
- file name with or without complete path and with or without extension- Returns:
- file name or path without extension
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getFileType
public static int getFileType(java.lang.String filename)
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getExtensionList
public java.util.ArrayList<java.lang.String> getExtensionList(int fileTypes)
- Parameters:
fileTypes
-- Returns:
- list of all extensions that are covered by fileTypes
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getExtension
public static java.lang.String getExtension(int filetype)
- Parameters:
filetype
-- Returns:
- file extension including the dot
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saveRXNFile
public void saveRXNFile(Reaction rxn)
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