charite.christo
Class ChPubmed

java.lang.Object
  charite.christo.ChPubmed

All Implemented Interfaces:

ChRunnable, java.awt.event.ActionListener, java.util.EventListener

public final class ChPubmed
extends java.lang.Object
implements ChRunnable, java.awt.event.ActionListener

HELP

Showing Abstracts

When the mouse hovers over a Pubmed reference of the form \"PMID:19762348\", the abstract is downloaded automatically in the background and shown in a certain text area. The same works for Uniprot identifiers of the form UNIPROT:Q9H936 or human Ensembl references of the form ENSG00000103064.

Showing Full-text

The user might associate a full PDF text with a Pubmed ID. Those Pubmed links are indicated by red background. The PDF can be looked at by using the context menu (right click). If the ALT-key is hold down while the mouse is moving over a Pubmed ID, then not the abstract, but the full text (without images) is shown.

The download directory

PDF-files are downloaded with the Web-browser into a certain directory. The program needs to know this directory. The PDF file that has been created at last in this directory is identified by the program and associated to the respective PMID.

Customizing the Browser

Many Web-browsers display PDF documents within the Browser's frame. With this behavior, the mechanism is not working. The browser must be configured such that PDF files are downloaded into a specific directory and displayed in an external PDF viewer such as WIKI:Evince or WIKI:Xpdf or WIKI:Acroread.

In Firefox browser go to Menu-bar>Edit>Preferences. The preferences frame will open. Click the Icon "Applications". A list with file types appear. Find the line "PDF document" and specify an action. A good choice which gives maximum control is "Always ask".

In other Web browsers customization works in a similar way.

Field Summary

static int	ABSTRACT
static java.lang.String	ACTION_FULL_TEXT_ASSOCIATED
static int	AUTO
static int	GO
static int	LIST
static int	PDF
static int	PDF_TITLE
static int	PDF2TXT
static long	SHOWABSTRACT_FULL_TEXT
static int	UNIPROT

Fields inherited from interface charite.christo.ChRunnable

APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT

Constructor Summary

ChPubmed()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
static java.io.File	dirSharedPdf()
static java.io.File	getDir(int type)
static java.io.File	getFile(java.lang.String w0, int type0)
static boolean	hasPdf(java.lang.String pmid)
static java.io.File	maybeDownload(java.lang.String w0)
static void	pdfRenameUseTitle(java.io.File dirP, java.lang.String fileSuffix)
static java.lang.String	pubmedTitle(int pmid)
static void	queueForDownload(java.lang.String id0, boolean isListPdf)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
static void	showAbstract(java.io.File f, ChTextComponents dest, long options)
static void	showPubmedPopup(java.lang.String pmid)
static java.lang.String	viaTest(java.net.URL u)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ACTION_FULL_TEXT_ASSOCIATED

public static final java.lang.String ACTION_FULL_TEXT_ASSOCIATED

See Also:

Constant Field Values

LIST

public static final int LIST

See Also:

Constant Field Values

PDF

public static final int PDF

See Also:

Constant Field Values

ABSTRACT

public static final int ABSTRACT

See Also:

Constant Field Values

UNIPROT

public static final int UNIPROT

See Also:

Constant Field Values

PDF2TXT

public static final int PDF2TXT

See Also:

Constant Field Values

GO

public static final int GO

See Also:

Constant Field Values

AUTO

public static final int AUTO

See Also:

Constant Field Values

PDF_TITLE

public static final int PDF_TITLE

See Also:

Constant Field Values

SHOWABSTRACT_FULL_TEXT

public static final long SHOWABSTRACT_FULL_TEXT

See Also:

Constant Field Values

Constructor Detail

ChPubmed

public ChPubmed()

Method Detail

queueForDownload

public static void queueForDownload(java.lang.String id0,
                                    boolean isListPdf)

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

Specified by:

run in interface ChRunnable

pdfRenameUseTitle

public static void pdfRenameUseTitle(java.io.File dirP,
                                     java.lang.String fileSuffix)

getFile

public static java.io.File getFile(java.lang.String w0,
                                   int type0)

hasPdf

public static boolean hasPdf(java.lang.String pmid)

getDir

public static java.io.File getDir(int type)

dirSharedPdf

public static java.io.File dirSharedPdf()

maybeDownload

public static java.io.File maybeDownload(java.lang.String w0)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

showPubmedPopup

public static void showPubmedPopup(java.lang.String pmid)

viaTest

public static java.lang.String viaTest(java.net.URL u)

pubmedTitle

public static java.lang.String pubmedTitle(int pmid)

showAbstract

public static void showAbstract(java.io.File f,
                                ChTextComponents dest,
                                long options)